diff --git a/docs/notebooks/external_sequences.ipynb b/docs/notebooks/external_sequences.ipynb
index 1b5152d9..c59aa186 100644
--- a/docs/notebooks/external_sequences.ipynb
+++ b/docs/notebooks/external_sequences.ipynb
@@ -178,7 +178,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "input=[] assembly_accession='GCF_000146045.2' sequence_accession='NC_001136.10' locus_tag='YDR294C' gene_id=851888 start=1049459 end=1053228 strand=-1\n",
+      "input=[] repository_id='NC_001136.10' coordinates=SimpleLocation(ExactPosition(1049458), ExactPosition(1053228), strand=-1) assembly_accession='GCF_000146045.2' locus_tag='YDR294C' gene_id=851888\n",
       "None\n",
       "╙── YDR294C (Dseqrecord(-3770))\n",
       "    └─╼ GenomeCoordinatesSource\n"
@@ -264,7 +264,7 @@
     {
      "data": {
       "text/plain": [
-       "RepositoryIdSource(input=[], repository_id='NC_001136.10', repository_name='genbank')"
+       "NCBISequenceSource(input=[], repository_id='NC_001136.10', coordinates=SimpleLocation(ExactPosition(1049458), ExactPosition(1053228), strand=-1))"
       ]
      },
      "execution_count": null,
diff --git a/poetry.lock b/poetry.lock
index 95da324e..079f7414 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-doc"
@@ -26,23 +26,22 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.11.0"
+version = "4.12.0"
 description = "High-level concurrency and networking framework on top of asyncio or Trio"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev", "test"]
 files = [
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-    {file = "anyio-4.11.0.tar.gz", hash = "sha256:82a8d0b81e318cc5ce71a5f1f8b5c4e63619620b63141ef8c995fa0db95a57c4"},
+    {file = "anyio-4.12.0-py3-none-any.whl", hash = "sha256:dad2376a628f98eeca4881fc56cd06affd18f659b17a747d3ff0307ced94b1bb"},
+    {file = "anyio-4.12.0.tar.gz", hash = "sha256:73c693b567b0c55130c104d0b43a9baf3aa6a31fc6110116509f27bf75e21ec0"},
 ]
 
 [package.dependencies]
 idna = ">=2.8"
-sniffio = ">=1.1"
 typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 
 [package.extras]
-trio = ["trio (>=0.31.0)"]
+trio = ["trio (>=0.31.0) ; python_version < \"3.10\"", "trio (>=0.32.0) ; python_version >= \"3.10\""]
 
 [[package]]
 name = "appdirs"
@@ -114,18 +113,18 @@ pycodestyle = ">=2.12.0"
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.14.2"
+version = "4.14.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.7.0"
 groups = ["main"]
 files = [
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+    {file = "beautifulsoup4-4.14.3-py3-none-any.whl", hash = "sha256:0918bfe44902e6ad8d57732ba310582e98da931428d231a5ecb9e7c703a735bb"},
+    {file = "beautifulsoup4-4.14.3.tar.gz", hash = "sha256:6292b1c5186d356bba669ef9f7f051757099565ad9ada5dd630bd9de5fa7fb86"},
 ]
 
 [package.dependencies]
-soupsieve = ">1.2"
+soupsieve = ">=1.6.1"
 typing-extensions = ">=4.0.0"
 
 [package.extras]
@@ -337,14 +336,14 @@ pycparser = {version = "*", markers = "implementation_name != \"PyPy\""}
 
 [[package]]
 name = "cfgv"
-version = "3.4.0"
+version = "3.5.0"
 description = "Validate configuration and produce human readable error messages."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev", "test"]
 files = [
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-    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+    {file = "cfgv-3.5.0-py2.py3-none-any.whl", hash = "sha256:a8dc6b26ad22ff227d2634a65cb388215ce6cc96bbcc5cfde7641ae87e8dacc0"},
+    {file = "cfgv-3.5.0.tar.gz", hash = "sha256:d5b1034354820651caa73ede66a6294d6e95c1b00acc5e9b098e917404669132"},
 ]
 
 [[package]]
@@ -392,104 +391,104 @@ test = ["pytest"]
 
 [[package]]
 name = "coverage"
-version = "7.11.3"
+version = "7.12.0"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.10"
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 ]
 
 [package.extras]
@@ -588,20 +587,20 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastapi"
-version = "0.121.2"
+version = "0.123.9"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
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 pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0 || >2.0.0,<2.0.1 || >2.0.1,<2.1.0 || >2.1.0,<3.0.0"
-starlette = ">=0.40.0,<0.50.0"
+starlette = ">=0.40.0,<0.51.0"
 typing-extensions = ">=4.8.0"
 
 [package.extras]
@@ -1038,22 +1037,24 @@ files = [
 
 [[package]]
 name = "networkx"
-version = "3.5"
+version = "3.6"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.11"
 groups = ["main"]
 files = [
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 ]
 
 [package.extras]
+benchmarking = ["asv", "virtualenv"]
 default = ["matplotlib (>=3.8)", "numpy (>=1.25)", "pandas (>=2.0)", "scipy (>=1.11.2)"]
 developer = ["mypy (>=1.15)", "pre-commit (>=4.1)"]
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 extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
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 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "pytest-xdist (>=3.0)"]
 test-extras = ["pytest-mpl", "pytest-randomly"]
 
@@ -1155,14 +1156,14 @@ files = [
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.8"
+version = "0.4.9"
 description = "A LinkML data model for OpenCloning"
 optional = false
 python-versions = "<4.0,>=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
@@ -1355,14 +1356,14 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "platformdirs"
-version = "4.5.0"
+version = "4.5.1"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "ipython", "test"]
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 ]
 
 [package.extras]
@@ -1560,14 +1561,14 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "2.12.4"
+version = "2.12.5"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 [package.dependencies]
@@ -1761,7 +1762,7 @@ wheel = "*"
 
 [[package]]
 name = "pydna"
-version = "5.5.4-post.16+e95e8603"
+version = "5.5.4-post.22+6f25090e"
 description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
 optional = false
 python-versions = ">=3.10,<4.0"
@@ -1777,7 +1778,7 @@ numpy = [
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     {version = ">=2.3.0", markers = "python_version >= \"3.12\""},
 ]
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+opencloning-linkml = "^0.4.9"
 prettytable = ">=3.5.0"
 pydivsufsort = ">=0.0.14"
 pyfiglet = "0.8.post1"
@@ -1788,13 +1789,13 @@ seguid = ">=0.0.5"
 clipboard = ["pyperclip (>=1.8.2)"]
 download = ["pyparsing (>=2.4.7)", "requests (>=2.26.0)"]
 express = ["cai2 (>=1.0.5)"]
-gel = ["matplotlib (>=3.4.3)", "pillow (>=8.4.0)", "scipy (>=1.11.3)", "scipy (>=1.9.3)"]
+gel = ["matplotlib (>=3.4.3)", "pillow (>=8.4.0)", "scipy (>=1.11.3) ; python_version >= \"3.12\"", "scipy (>=1.9.3) ; python_version < \"3.12\""]
 
 [package.source]
 type = "git"
 url = "https://github.com/pydna-group/pydna"
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-resolved_reference = "e95e8603b082e50b7873eab0ae1f8abf7b4d25bc"
+reference = "6f25090ec653e38219021aa46fa4440f888e958c"
+resolved_reference = "6f25090ec653e38219021aa46fa4440f888e958c"
 
 [[package]]
 name = "pyfiglet"
@@ -2256,127 +2257,127 @@ httpx = ">=0.25.0"
 
 [[package]]
 name = "rpds-py"
-version = "0.29.0"
+version = "0.30.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.10"
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+    {file = "rpds_py-0.30.0-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl", hash = "sha256:ac37f9f516c51e5753f27dfdef11a88330f04de2d564be3991384b2f3535d02e"},
+    {file = "rpds_py-0.30.0.tar.gz", hash = "sha256:dd8ff7cf90014af0c0f787eea34794ebf6415242ee1d6fa91eaba725cc441e84"},
 ]
 
 [[package]]
@@ -2406,18 +2407,6 @@ files = [
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
-[[package]]
-name = "sniffio"
-version = "1.3.1"
-description = "Sniff out which async library your code is running under"
-optional = false
-python-versions = ">=3.7"
-groups = ["main", "dev", "test"]
-files = [
-    {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"},
-    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
-]
-
 [[package]]
 name = "soupsieve"
 version = "2.8"
@@ -2452,14 +2441,14 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "starlette"
-version = "0.49.3"
+version = "0.50.0"
 description = "The little ASGI library that shines."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "starlette-0.49.3-py3-none-any.whl", hash = "sha256:b579b99715fdc2980cf88c8ec96d3bf1ce16f5a8051a7c2b84ef9b1cdecaea2f"},
-    {file = "starlette-0.49.3.tar.gz", hash = "sha256:1c14546f299b5901a1ea0e34410575bc33bbd741377a10484a54445588d00284"},
+    {file = "starlette-0.50.0-py3-none-any.whl", hash = "sha256:9e5391843ec9b6e472eed1365a78c8098cfceb7a74bfd4d6b1c0c0095efb3bca"},
+    {file = "starlette-0.50.0.tar.gz", hash = "sha256:a2a17b22203254bcbc2e1f926d2d55f3f9497f769416b3190768befe598fa3ca"},
 ]
 
 [package.dependencies]
@@ -2705,4 +2694,4 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
 [metadata]
 lock-version = "2.1"
 python-versions = "^3.11"
-content-hash = "89226063947f0a896117295107fb190439a215ea4cc28756d8de77c6496249d3"
+content-hash = "66cafb4bdee008393fc8504786d074cd2ba9d54a88978de413825a42ba8b69d5"
diff --git a/pyproject.toml b/pyproject.toml
index c8796d82..d411499b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,12 +25,11 @@ pydantic = "^2.7.1"
 pandas = "^2.2.3"
 openpyxl = "^3.1.5"
 pyyaml = "^6.0.2"
-opencloning-linkml = "0.4.8"
 primer3-py = "2.2.0"
 biopython = "^1.85"
 packaging = "^25.0"
 pairwise-alignments-to-msa = "^0.1.1"
-pydna = {git = "https://github.com/pydna-group/pydna", rev = "e95e8603b082e50b7873eab0ae1f8abf7b4d25bc"}
+pydna = {git = "https://github.com/pydna-group/pydna", rev = "6f25090ec653e38219021aa46fa4440f888e958c"}
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.0.4"
diff --git a/src/opencloning/app_settings.py b/src/opencloning/app_settings.py
index 9a25e7e4..3dba6848 100644
--- a/src/opencloning/app_settings.py
+++ b/src/opencloning/app_settings.py
@@ -22,6 +22,11 @@ def parse_bool(value: str) -> bool:
 
 # External services settings =================================
 NCBI_API_KEY = os.environ.get('NCBI_API_KEY')
+NCBI_MAX_SEQUENCE_LENGTH = (
+    int(os.environ.get('NCBI_MAX_SEQUENCE_LENGTH'))
+    if os.environ.get('NCBI_MAX_SEQUENCE_LENGTH') is not None
+    else 500000
+)
 PLANNOTATE_URL = os.environ['PLANNOTATE_URL'] if 'PLANNOTATE_URL' in os.environ else None
 PLANNOTATE_TIMEOUT = int(os.environ['PLANNOTATE_TIMEOUT']) if 'PLANNOTATE_TIMEOUT' in os.environ else 20
 # Handle trailing slash:
@@ -58,6 +63,7 @@ class Settings(BaseModel):
     BATCH_CLONING: bool
     RECORD_STUBS: bool
     NCBI_API_KEY: str | None
+    NCBI_MAX_SEQUENCE_LENGTH: int
     ALLOWED_ORIGINS: list[str]
     PLANNOTATE_URL: str | None
     PLANNOTATE_TIMEOUT: int
@@ -73,6 +79,7 @@ class Settings(BaseModel):
     BATCH_CLONING=BATCH_CLONING,
     RECORD_STUBS=RECORD_STUBS,
     NCBI_API_KEY=NCBI_API_KEY,
+    NCBI_MAX_SEQUENCE_LENGTH=NCBI_MAX_SEQUENCE_LENGTH,
     ALLOWED_ORIGINS=ALLOWED_ORIGINS,
     PLANNOTATE_URL=PLANNOTATE_URL,
     PLANNOTATE_TIMEOUT=PLANNOTATE_TIMEOUT,
diff --git a/src/opencloning/batch_cloning/pombe/pombe_clone.py b/src/opencloning/batch_cloning/pombe/pombe_clone.py
index e6986bcf..940290c0 100644
--- a/src/opencloning/batch_cloning/pombe/pombe_clone.py
+++ b/src/opencloning/batch_cloning/pombe/pombe_clone.py
@@ -1,36 +1,34 @@
 import os
-from opencloning.endpoints.external_import import genome_coordinates, get_from_repository_id_addgene, read_from_file
-from opencloning.endpoints.assembly import pcr, homologous_recombination
-from opencloning.pydantic_models import BaseCloningStrategy
-
-from opencloning_linkml.datamodel import (
-    GenomeCoordinatesSource,
-    AddgeneIdSource,
-    PCRSource,
-    Primer as PrimerModel,
-    HomologousRecombinationSource,
-    UploadedFileSource,
-    TextFileSequence,
-)
-
-from opencloning.ncbi_requests import get_annotations_from_query
+from pydna.assembly2 import homologous_recombination_integration, pcr_assembly
+from opencloning.dna_functions import request_from_addgene
+from opencloning.ncbi_requests import get_annotations_from_query, get_genome_region_from_annotation
 import asyncio
-import json
 from Bio import SeqIO
+from pydna.primer import Primer
+from pydna.opencloning_models import CloningStrategy
+from fastapi.datastructures import UploadFile
 from pydna.parsers import parse as pydna_parse
 
 
 async def main(
-    gene: str, assembly_accession: str, output_dir: str, plasmid: str | dict = '19343', padding: int = 1000
+    gene: str,
+    assembly_accession: str,
+    output_dir: str,
+    plasmid_input: UploadFile | str = '19343',
+    padding: int = 1000,
 ):
     print(f"\033[92mCloning {gene}\033[0m")
     # Parse primers =================================================================================
-    primer_records = list(SeqIO.parse(os.path.join(output_dir, gene, 'primers.fa'), 'fasta'))
-    checking_primers = list(SeqIO.parse(os.path.join(output_dir, 'checking_primers.fa'), 'fasta'))
-    primer_records = primer_records[:3] + checking_primers[1:] + primer_records[3:] + checking_primers[:1]
-    primers = []
-    for primer in primer_records:
-        primers.append(PrimerModel(sequence=str(primer.seq), id=0, name=primer.id))
+    primers = [Primer(p) for p in SeqIO.parse(os.path.join(output_dir, gene, 'primers.fa'), 'fasta')]
+    common_primers = [Primer(p) for p in SeqIO.parse(os.path.join(output_dir, 'checking_primers.fa'), 'fasta')]
+
+    # Get plasmid sequence =================================================================================
+    if isinstance(plasmid_input, UploadFile):
+        file_content = (await plasmid_input.read()).decode()
+
+        plasmid = pydna_parse(file_content)[0]
+    else:
+        plasmid = await request_from_addgene(plasmid_input)
 
     # Get genome region =====================================================================
     annotations = await get_annotations_from_query(gene, assembly_accession)
@@ -41,104 +39,24 @@ async def main(
     if len(annotations) != 1:
         raise ValueError(f'No right annotation found for {gene}')
 
-    annotation = annotations[0]
-
-    gene_range = annotation['genomic_regions'][0]['gene_range']['range'][0]
-    sequence_accession = annotation['genomic_regions'][0]['gene_range']['accession_version']
-    locus_tag = annotation.get('locus_tag', None)
-    gene_id = annotation.get('gene_id', None)
-    start = int(gene_range['begin'])
-    end = int(gene_range['end'])
-    orientation = 1 if gene_range['orientation'] == 'plus' else -1
-
-    source = GenomeCoordinatesSource(
-        id=0,
-        start=start - padding,
-        end=end + padding,
-        strand=orientation,
-        assembly_accession=assembly_accession,
-        sequence_accession=sequence_accession,
-        locus_tag=locus_tag,
-        gene_id=gene_id,
-        output_name=gene,
-    )
-    locus = await genome_coordinates(source)
-
-    cloning_strategy = BaseCloningStrategy(
-        sequences=[],
-        sources=[],
-        primers=[],
-        description=f'Cloning strategy for deleting the gene {gene} using PCR and homologous recombination',
-    )
-    for primer in primers:
-        cloning_strategy.add_primer(primer)
-    locus_seq: TextFileSequence = TextFileSequence.model_validate(locus['sequences'][0])
-    locus_source: GenomeCoordinatesSource = GenomeCoordinatesSource.model_validate(locus['sources'][0])
-    cloning_strategy.add_source_and_sequence(locus_source, locus_seq)
-
-    # Get plasmid sequence =================s================================================================
-    if not isinstance(plasmid, str):
-        if plasmid.filename.endswith('.fa') or plasmid.filename.endswith('.fasta'):
-            resp = await read_from_file(plasmid, None, None, True, None, None, None)
-        else:
-            resp = await read_from_file(plasmid, None, None, None, None, None, None)
-        # Verify that plasmid is circular
-        if not pydna_parse(resp['sequences'][0].file_content)[0].circular:
-            raise ValueError('Plasmid is not circular')
-        plasmid_source: UploadedFileSource = UploadedFileSource.model_validate(resp['sources'][0])
-    else:
-        addgene_source = AddgeneIdSource(
-            id=0,
-            repository_id=plasmid,
-            repository_name='addgene',
-        )
-        resp = await get_from_repository_id_addgene(addgene_source)
-        plasmid_source: AddgeneIdSource = AddgeneIdSource.model_validate(resp['sources'][0])
-
-    plasmid_seq: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
-    cloning_strategy.add_source_and_sequence(plasmid_source, plasmid_seq)
+    locus = await get_genome_region_from_annotation(annotations[0], 1000, 1000)
 
     # PCR ================================================================================================
-    pcr_source = PCRSource(id=0, output_name='amplified_marker')
-    resp = await pcr(pcr_source, [plasmid_seq], [primers[0], primers[1]], 15, 0)
+    pcr_products = pcr_assembly(plasmid, primers[0], primers[1], limit=14, mismatches=0)
+    pcr_products[0].name = 'amplified_marker'
+    alleles = homologous_recombination_integration(locus, [pcr_products[0]], 40)
+    pcr_check1 = pcr_assembly(alleles[0], primers[2], common_primers[1], limit=14, mismatches=0)[0]
+    pcr_check1.name = 'check_pcr_left'
+    pcr_check2 = pcr_assembly(alleles[0], primers[3], common_primers[0], limit=14, mismatches=0)[0]
+    pcr_check2.name = 'check_pcr_right'
 
-    pcr_product: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
-    pcr_source: PCRSource = PCRSource.model_validate(resp['sources'][0])
-    cloning_strategy.add_source_and_sequence(pcr_source, pcr_product)
-
-    # Homologous recombination ========================================================================
-    hrec_source = HomologousRecombinationSource(id=0, output_name='deletion_allele')
-    resp = await homologous_recombination(hrec_source, [locus_seq, pcr_product], 50)
-
-    hrec_product: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
-    hrec_source: HomologousRecombinationSource = HomologousRecombinationSource.model_validate(resp['sources'][0])
-    cloning_strategy.add_source_and_sequence(hrec_source, hrec_product)
-
-    # Checking pcr 1 ======================================================================================
-    check_pcr_source_left = PCRSource(id=0, output_name='check_pcr_left')
-    resp = await pcr(check_pcr_source_left, [hrec_product], [primers[2], primers[3]], 15, 0)
-
-    check_pcr_product_left: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
-    check_pcr_source_left: PCRSource = PCRSource.model_validate(resp['sources'][0])
-    cloning_strategy.add_source_and_sequence(check_pcr_source_left, check_pcr_product_left)
-
-    # Checking pcr 2 ======================================================================================
-    check_pcr_source_right = PCRSource(id=0, output_name='check_pcr_right')
-    resp = await pcr(check_pcr_source_right, [hrec_product], [primers[4], primers[5]], 15, 0)
-
-    check_pcr_product_right: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
-    check_pcr_source_right: PCRSource = PCRSource.model_validate(resp['sources'][0])
-    cloning_strategy.add_source_and_sequence(check_pcr_source_right, check_pcr_product_right)
-
-    cloning_strategy.description = (
-        f'Cloning strategy for deleting the gene {gene} using PCR and homologous recombination'
-    )
+    cs = CloningStrategy.from_dseqrecords([pcr_check1, pcr_check2])
 
     if not os.path.exists(os.path.join(output_dir, gene)):
         os.makedirs(os.path.join(output_dir, gene))
 
     with open(os.path.join(output_dir, gene, 'cloning_strategy.json'), 'w') as f:
-        json.dump(cloning_strategy.model_dump(), f, indent=2)
+        f.write(cs.model_dump_json(indent=2))
 
 
 if __name__ == '__main__':
diff --git a/src/opencloning/batch_cloning/pombe/pombe_summary.py b/src/opencloning/batch_cloning/pombe/pombe_summary.py
index 65fa4c6a..0532608e 100644
--- a/src/opencloning/batch_cloning/pombe/pombe_summary.py
+++ b/src/opencloning/batch_cloning/pombe/pombe_summary.py
@@ -40,16 +40,17 @@ def process_folder(working_dir: str):
     # We do this to have action to .end and .start
     pcr_sources = [PCRSource.model_validate(s.model_dump()) for s in pcr_sources]
     locus_source = next(s for s in strategy.sources if s.type == 'GenomeCoordinatesSource')
+    locus_location = Location.fromstring(locus_source.coordinates)
     hrec_source = next(s for s in strategy.sources if s.type == 'HomologousRecombinationSource')
     # We do this to have action to .end and .start
     hrec_source: HomologousRecombinationSource = HomologousRecombinationSource.model_validate(hrec_source.model_dump())
 
-    chromosome = chromosomes[locus_source.sequence_accession]
+    chromosome = chromosomes[locus_source.repository_id]
     insertion_start = (
-        locus_source.start + location_boundaries(Location.fromstring(hrec_source.input[0].right_location))[1]
+        locus_location.start + location_boundaries(Location.fromstring(hrec_source.input[0].right_location))[1]
     )
     insertion_end = (
-        locus_source.start + location_boundaries(Location.fromstring(hrec_source.input[-1].left_location))[0]
+        locus_location.start + location_boundaries(Location.fromstring(hrec_source.input[-1].left_location))[0]
     )
 
     # Write out the sequences in genbank format and extract some relevant info
diff --git a/src/opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json b/src/opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json
index b35d146b..7dfe99b3 100644
--- a/src/opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json
+++ b/src/opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json
@@ -81,7 +81,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "71287",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/352460/6c8b0369-e549-4517-95da-8d07146ca49d/addgene-plasmid-71287-sequence-352460.gbk",
       "addgene_sequence_type": "addgene-full"
     },
@@ -92,7 +91,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "71287",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/352460/6c8b0369-e549-4517-95da-8d07146ca49d/addgene-plasmid-71287-sequence-352460.gbk",
       "addgene_sequence_type": "addgene-full"
     },
@@ -103,7 +101,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "213912",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/437264/8bd82b44-a1c3-4f81-8936-ebcc16d171e9/addgene-plasmid-213912-sequence-437264.gbk",
       "addgene_sequence_type": "addgene-full"
     },
@@ -114,7 +111,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "213913",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/437263/af62d64e-1f22-4dce-aafa-7935d1665700/addgene-plasmid-213913-sequence-437263.gbk",
       "addgene_sequence_type": "addgene-full"
     },
@@ -125,7 +121,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "133748",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/271264/c0ae5f43-46e6-4175-a0c1-9a00cbb92034/addgene-plasmid-133748-sequence-271264.gbk",
       "addgene_sequence_type": "addgene-full"
     },
@@ -135,8 +130,7 @@
       "output_name": "pDONR_P2r-P3",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pDONR_P2r-P3",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pDONR_P2r-P3"
     },
     {
       "id": 7,
@@ -207,7 +201,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "63143",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/223326/8c81fe9a-fb57-40bc-93d6-e17d83502061/addgene-plasmid-63143-sequence-223326.gbk",
       "addgene_sequence_type": "addgene-full"
     }
@@ -258,7 +251,7 @@
   ],
   "description": "",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/src/opencloning/endpoints/external_import.py b/src/opencloning/endpoints/external_import.py
index 1b03ec7c..10e0d712 100644
--- a/src/opencloning/endpoints/external_import.py
+++ b/src/opencloning/endpoints/external_import.py
@@ -1,4 +1,5 @@
 from fastapi import Body, Query, HTTPException, Response, UploadFile, File
+from opencloning.app_settings import settings
 from pydantic import create_model
 import io
 import warnings
@@ -25,6 +26,7 @@
     SequenceFileFormat,
     SEVASource,
     OpenDNACollectionsSource,
+    NCBISequenceSource,
 )
 from pydna.opencloning_models import SequenceLocationStr
 from ..dna_functions import (
@@ -245,31 +247,41 @@ def handle_repository_errors(exception: Exception, repository_name: str) -> None
 )
 async def get_from_repository_id(
     source: (
-        RepositoryIdSource
-        | AddgeneIdSource
+        AddgeneIdSource
         | BenchlingUrlSource
         | SnapGenePlasmidSource
         | EuroscarfSource
         | WekWikGeneIdSource
         | SEVASource
         | OpenDNACollectionsSource
+        | NCBISequenceSource
     ),
 ):
-    return RedirectResponse(f'/repository_id/{source.repository_name}', status_code=307)
+    mapping_dict = {
+        'AddgeneIdSource': 'addgene',
+        'BenchlingUrlSource': 'benchling',
+        'SnapGenePlasmidSource': 'snapgene',
+        'EuroscarfSource': 'euroscarf',
+        'WekWikGeneIdSource': 'wekwikgene',
+        'SEVASource': 'seva',
+        'OpenDNACollectionsSource': 'open_dna_collections',
+        'NCBISequenceSource': 'genbank',
+    }
+    return RedirectResponse(f'/repository_id/{mapping_dict[source.type]}', status_code=307)
 
 
 @router.post(
     '/repository_id/genbank',
     response_model=create_model(
-        'RepositoryIdResponse', sources=(list[RepositoryIdSource], ...), sequences=(list[TextFileSequence], ...)
+        'RepositoryIdResponse', sources=(list[NCBISequenceSource], ...), sequences=(list[TextFileSequence], ...)
     ),
 )
-async def get_from_repository_id_genbank(source: RepositoryIdSource):
+async def get_from_repository_id_genbank(source: NCBISequenceSource):
     try:
         # This request already fails if the sequence does not exist
         seq_length = await ncbi_requests.get_sequence_length_from_sequence_accession(source.repository_id)
-        if seq_length > 100000:
-            raise HTTPException(400, 'sequence is too long (max 100000 bp)')
+        if seq_length > settings.NCBI_MAX_SEQUENCE_LENGTH:
+            raise HTTPException(400, f'sequence is too long (max {settings.NCBI_MAX_SEQUENCE_LENGTH} bp)')
         seq = await ncbi_requests.get_genbank_sequence(source.repository_id)
     except Exception as exception:
         handle_repository_errors(exception, 'NCBI')
@@ -287,7 +299,7 @@ async def get_from_repository_id_addgene(source: AddgeneIdSource):
     try:
         dseq = await request_from_addgene(source.repository_id)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'Addgene')
 
     return format_products(
         source.id,
@@ -314,7 +326,7 @@ async def get_from_repository_id_wekwikgene(source: WekWikGeneIdSource):
     try:
         dseq = await request_from_wekwikgene(source.repository_id)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'WeKwikGene')
     return format_products(
         source.id,
         [dseq],
@@ -342,7 +354,7 @@ async def get_from_benchling_url(
         dseq = await get_sequence_from_benchling_url(source.repository_id)
         return format_products(source.id, [dseq], None, source.output_name)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'Benchling')
 
 
 @router.post(
@@ -359,7 +371,7 @@ async def get_from_repository_id_snapgene(
         seq = await request_from_snapgene(plasmid_set, plasmid_name)
         return format_products(source.id, [seq], None, source.output_name)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'Snapgene')
 
 
 @router.post(
@@ -377,7 +389,7 @@ async def get_from_repository_id_euroscarf(source: EuroscarfSource):
         dseq = await get_sequence_from_euroscarf_url(source.repository_id)
         return format_products(source.id, [dseq], None, source.output_name)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'Euroscarf')
 
 
 @router.post(
@@ -402,7 +414,7 @@ async def get_from_repository_id_igem(source: IGEMSource):
             ''',
         )
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'iGEM')
 
 
 @router.post(
@@ -431,7 +443,7 @@ async def get_from_repository_id_open_dna_collections(source: OpenDNACollections
             ''',
         )
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'OpenDNA Collections')
 
 
 @router.post(
@@ -445,7 +457,16 @@ async def genome_coordinates(
 ):
 
     # Validate that coordinates make sense
-    ncbi_requests.validate_coordinates_pre_request(source.start, source.end, source.strand)
+    try:
+        location_str = SequenceLocationStr(source.coordinates)
+        location = location_str.to_biopython_location()
+        start, end, strand = location_str.get_ncbi_format_coordinates()
+    except Exception as e:
+        raise HTTPException(422, f'Invalid coordinates: {e}') from e
+
+    if len(location) > settings.NCBI_MAX_SEQUENCE_LENGTH:
+        raise HTTPException(400, f'sequence is too long (max {settings.NCBI_MAX_SEQUENCE_LENGTH} bp)')
+
     if source.locus_tag is not None and source.assembly_accession is None:
         raise HTTPException(422, 'assembly_accession is required if locus_tag is set')
 
@@ -453,7 +474,12 @@ async def genome_coordinates(
     async def validate_locus_task():
         if source.locus_tag is not None:
             return await ncbi_requests.validate_locus_tag(
-                source.locus_tag, source.assembly_accession, source.gene_id, source.start, source.end, source.strand
+                source.locus_tag,
+                source.assembly_accession,
+                source.gene_id,
+                start,
+                end,
+                strand,
             )
 
     async def validate_assembly_task():
@@ -462,16 +488,14 @@ async def validate_assembly_task():
             sequence_accessions = await ncbi_requests.get_sequence_accessions_from_assembly_accession(
                 source.assembly_accession
             )
-            if source.sequence_accession not in sequence_accessions:
+            if source.repository_id not in sequence_accessions:
                 raise HTTPException(
                     400,
-                    f'Sequence accession {source.sequence_accession} not contained in assembly accession {source.assembly_accession}, which contains accessions: {", ".join(sequence_accessions)}',
+                    f'Sequence accession {source.repository_id} not contained in assembly accession {source.assembly_accession}, which contains accessions: {", ".join(sequence_accessions)}',
                 )
 
     async def get_sequence_task():
-        return await ncbi_requests.get_genbank_sequence(
-            source.sequence_accession, source.start, source.end, source.strand
-        )
+        return await ncbi_requests.get_genbank_sequence(source.repository_id, start, end, strand)
 
     tasks = [validate_locus_task(), validate_assembly_task(), get_sequence_task()]
 
@@ -483,7 +507,7 @@ async def get_sequence_task():
     source.gene_id = gene_id
 
     # NCBI does not complain for coordinates that fall out of the sequence, so we have to check here
-    if len(seq) != source.end - source.start + 1:
+    if len(seq) != len(location):
         raise HTTPException(400, 'coordinates fall outside the sequence')
 
     return {'sequences': [format_sequence_genbank(seq, source.output_name)], 'sources': [source.model_copy()]}
@@ -502,7 +526,7 @@ async def get_from_repository_id_seva(source: SEVASource):
     try:
         dseq = await get_seva_plasmid(source.repository_id)
     except Exception as exception:
-        handle_repository_errors(exception, source.repository_name)
+        handle_repository_errors(exception, 'SEVA')
 
     return format_products(
         source.id,
diff --git a/src/opencloning/endpoints/no_input.py b/src/opencloning/endpoints/no_input.py
index 89a6efc4..84357e5a 100644
--- a/src/opencloning/endpoints/no_input.py
+++ b/src/opencloning/endpoints/no_input.py
@@ -16,6 +16,7 @@
     TextFileSequence,
     ManuallyTypedSource,
     OligoHybridizationSource,
+    ManuallyTypedSequence,
 )
 
 from .. import request_examples
@@ -30,17 +31,14 @@
         'ManuallyTypedResponse', sources=(list[ManuallyTypedSource], ...), sequences=(list[TextFileSequence], ...)
     ),
 )
-async def manually_typed(source: ManuallyTypedSource):
+async def manually_typed(source: ManuallyTypedSource, sequence: ManuallyTypedSequence):
     """Return the sequence from a manually typed sequence"""
-    if source.circular:
-        # TODO: This should be done in the model validator
-        if source.overhang_crick_3prime != 0 or source.overhang_watson_3prime != 0:
-            raise HTTPException(422, 'Circular sequences cannot have overhangs.')
-        seq = Dseqrecord(source.user_input, circular=source.circular)
+    if sequence.circular:
+        seq = Dseqrecord(sequence.sequence, circular=sequence.circular)
     else:
         seq = Dseqrecord(
             Dseq.from_full_sequence_and_overhangs(
-                source.user_input, source.overhang_crick_3prime, source.overhang_watson_3prime
+                sequence.sequence, sequence.overhang_crick_3prime, sequence.overhang_watson_3prime
             )
         )
     return {'sequences': [format_sequence_genbank(seq, source.output_name)], 'sources': [source]}
diff --git a/src/opencloning/ncbi_requests.py b/src/opencloning/ncbi_requests.py
index bb17b9ea..d947ca08 100644
--- a/src/opencloning/ncbi_requests.py
+++ b/src/opencloning/ncbi_requests.py
@@ -1,7 +1,8 @@
 from fastapi import HTTPException
 import math
 from pydna.dseqrecord import Dseqrecord
-from pydna.opencloning_models import RepositoryIdSource, GenomeCoordinatesSource
+from pydna.opencloning_models import GenomeCoordinatesSource, NCBISequenceSource
+from Bio.SeqFeature import Location
 
 from .app_settings import settings
 from .http_client import get_http_client, Response
@@ -90,6 +91,10 @@ async def get_sequence_length_from_sequence_accession(sequence_accession: str) -
 async def get_genbank_sequence(sequence_accession, start=None, end=None, strand=None) -> Dseqrecord:
     from opencloning.dna_functions import get_sequences_from_file_url
 
+    # Ensure that start, end, and strand are either all None or none are None
+    if (start is None or end is None or strand is None) and not (start is None and end is None and strand is None):
+        raise ValueError('start, end, and strand must either all be None or none be None')
+
     gb_strand = 1 if strand == 1 or strand is None else 2
     url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
     params = {
@@ -116,20 +121,16 @@ async def get_genbank_sequence(sequence_accession, start=None, end=None, strand=
     except Exception as e:
         raise e
 
-    seq.source = RepositoryIdSource(repository_name='genbank', repository_id=sequence_accession)
-    return seq
-
+    if start is not None:
+        if strand == -1:
+            location = Location.fromstring(f'complement({start}..{end})')
+        else:
+            location = Location.fromstring(f'{start}..{end}')
+    else:
+        location = None
 
-def validate_coordinates_pre_request(start, end, strand):
-    # TODO: move this to the class
-    if strand not in [1, -1]:
-        raise HTTPException(422, 'strand must be 1 or -1')
-    if start >= end:
-        raise HTTPException(422, 'start must be less than end')
-    if start < 1:
-        raise HTTPException(422, 'start must be greater than 0')
-    if end - start > 100000:
-        raise HTTPException(400, 'sequence is too long (max 100000 bp)')
+    seq.source = NCBISequenceSource(repository_id=sequence_accession, coordinates=location)
+    return seq
 
 
 def get_info_from_annotation(annotation: dict) -> dict:
@@ -171,7 +172,10 @@ async def validate_locus_tag(
 
     # The gene should fall within the range (range might be bigger if bases were requested upstream or downstream)
     if gene_start < start or gene_end > end or gene_strand != strand:
-        raise HTTPException(400, f'wrong coordinates, expected to fall within {start}, {end} on strand: {strand}')
+        raise HTTPException(
+            400,
+            f'wrong coordinates, the gene should fall within the requested coordinates, {start}, {end} on strand: {strand}',
+        )
 
     return gene_id
 
@@ -185,14 +189,14 @@ async def get_genome_region_from_annotation(
     start = start - padding_left
     end = end + padding_right
     seq = await get_genbank_sequence(sequence_accession, start, end, strand)
+    location_str = f'{start}..{end}' if strand != -1 else f'complement({start}..{end})'
+    coordinates = Location.fromstring(location_str)
     source = GenomeCoordinatesSource(
         assembly_accession=assembly_accession,
-        sequence_accession=sequence_accession,
+        repository_id=sequence_accession,
+        coordinates=coordinates,
         locus_tag=locus_tag,
         gene_id=gene_id,
-        start=start,
-        end=end,
-        strand=strand,
     )
     seq.name = locus_tag
     seq.source = source
diff --git a/src/opencloning/request_examples.py b/src/opencloning/request_examples.py
index 7fe500c3..d4781b1a 100644
--- a/src/opencloning/request_examples.py
+++ b/src/opencloning/request_examples.py
@@ -3,58 +3,48 @@
         'summary': 'All parameters provided',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
+            'repository_id': 'NC_003424.3',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
             'gene_id': 2543372,
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'full_with_genbank_accession': {
         'summary': 'All parameters provided, but sequence accession is GenBank',
         'value': {
             'id': 1,
-            'sequence_accession': 'CU329670.1',
+            'repository_id': 'CU329670.1',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
             'gene_id': 2543372,
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'id_omitted': {
         'summary': 'Gene ID omitted (filled in response)',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
+            'repository_id': 'NC_003424.3',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'assembly_accession_omitted': {
         'summary': 'Sequence accession only',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'repository_id': 'NC_003424.3',
+            'coordinates': '1877009..1881726',
         },
     },
     'viral_sequence': {
         'summary': 'Viral sequence not associated with assembly',
         'value': {
             'id': 1,
-            'sequence_accession': 'DQ208311.2',
-            'start': 20,
-            'end': 2050,
-            'strand': -1,
+            'repository_id': 'DQ208311.2',
+            'coordinates': 'complement(20..2050)',
         },
     },
 }
@@ -84,7 +74,6 @@
         'summary': 'Typical example',
         'value': {
             'id': 0,
-            'repository_name': 'benchling',
             'repository_id': 'https://benchling.com/siverson/f/lib_B94YxDHhQh-cidar-moclo-library/seq_kryGidaz-c0062_cd.gb',
         },
     },
@@ -95,7 +84,6 @@
         'summary': 'Typical example',
         'value': {
             'id': 0,
-            'repository_name': 'snapgene',
             'repository_id': 'basic_cloning_vectors/pEASY-T1_(linearized)',
         },
     },
diff --git a/tests/test_endpoints_external_import.py b/tests/test_endpoints_external_import.py
index 9e552406..a4d50666 100644
--- a/tests/test_endpoints_external_import.py
+++ b/tests/test_endpoints_external_import.py
@@ -13,7 +13,7 @@
 from opencloning.dna_functions import read_dsrecord_from_json
 import opencloning.main as _main
 from opencloning_linkml.datamodel import (
-    RepositoryIdSource,
+    NCBISequenceSource,
     TextFileSequence,
     UploadedFileSource,
     GenomeCoordinatesSource,
@@ -301,9 +301,8 @@ class GenBankTest(unittest.TestCase):
     # TODO these tests will not work off-line, so the case where connection cannot be established should be handled in some way
     def test_request_gene(self):
         """Test whether the gene is requested from GenBank"""
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='NM_001018957.2',
         )
         response = client.post('/repository_id/genbank', json=source.model_dump())
@@ -314,9 +313,8 @@ def test_request_gene(self):
 
     def test_request_wrong_id(self):
         """Test a wrong Genbank id"""
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='wrong_id',
         )
         response = client.post('/repository_id/genbank', json=source.model_dump())
@@ -331,9 +329,8 @@ def test_request_wrong_id2(self):
         )
         # 400 is the error code for a wrong sequence accession :_)
         respx.get('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi').respond(400, text='')
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='wrong_id',
         )
         response = client.post('/repository_id/genbank', json=source.model_dump())
@@ -347,9 +344,8 @@ def test_eutils_down(self):
         respx.get('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi').mock(
             side_effect=httpx.ConnectError('Connection error')
         )
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='NM_001018957.2',
         )
         response = client.post('/repository_id/genbank', json=source.model_dump())
@@ -367,9 +363,8 @@ def test_eutils_down(self):
 
     def test_redirect(self):
         """The repository_id endpoint should redirect based on repository_name value"""
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='NM_001018957.2',
         )
         response = client.post('/repository_id', json=source.model_dump())
@@ -380,9 +375,8 @@ def test_redirect(self):
 
     def test_rename(self):
         """If passing output_name, it renames the output"""
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='NM_001018957.2',
             output_name='hello',
         )
@@ -394,9 +388,8 @@ def test_rename(self):
 
     def test_long_sequence(self):
         """Test that a long sequence raises an error"""
-        source = RepositoryIdSource(
+        source = NCBISequenceSource(
             id=1,
-            repository_name='genbank',
             repository_id='CU329670.1',
         )
         response = client.post('/repository_id/genbank', json=source.model_dump())
@@ -424,7 +417,6 @@ def test_request_plasmid(self):
         for example in examples:
             source = AddgeneIdSource(
                 id=1,
-                repository_name='addgene',
                 repository_id=example['id'],
             )
 
@@ -451,7 +443,6 @@ def test_old_url(self):
         """Works for an Addgene url that has now been replaced by a newer one"""
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='65109',
             addgene_sequence_type='addgene-full',
             sequence_file_url='https://media.addgene.org/snapgene-media/v1.7.9-0-g88a3305/sequences/110162/c1c98803-c8ba-44a6-95b8-d6a94097e36f/addgene-plasmid-65109-sequence-110162.gbk',
@@ -477,7 +468,6 @@ def test_missing_sequences(self):
         # Non-existing id
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='DUMMYTEST',
         )
 
@@ -488,7 +478,6 @@ def test_missing_sequences(self):
         # Id that has no full-sequences
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='39291',
         )
         response = client.post('/repository_id/addgene', json=source.model_dump())
@@ -498,7 +487,6 @@ def test_missing_sequences(self):
         # url does not exist
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='39282',
             sequence_file_url='https://media.addgene.org/snapgene-media/wrongggggggg.gbk',
         )
@@ -509,7 +497,6 @@ def test_redirect(self):
         """Test repository_id endpoint should redirect based on repository_name value"""
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='39282',
         )
         response = client.post('/repository_id', json=source.model_dump())
@@ -523,12 +510,11 @@ def test_addgene_down(self):
         respx.get('https://www.addgene.org/39282/sequences/').mock(side_effect=httpx.ConnectError('Connection error'))
         source = AddgeneIdSource(
             id=1,
-            repository_name='addgene',
             repository_id='39282',
         )
         response = client.post('/repository_id/addgene', json=source.model_dump())
         self.assertEqual(response.status_code, 504)
-        self.assertIn('Unable to connect to addgene', response.json()['detail'])
+        self.assertIn('Unable to connect to Addgene', response.json()['detail'])
 
 
 class WekWikGeneSourceTest(unittest.TestCase):
@@ -536,7 +522,6 @@ class WekWikGeneSourceTest(unittest.TestCase):
     def test_valid_id(self):
         source = WekWikGeneIdSource(
             id=1,
-            repository_name='wekwikgene',
             repository_id='0000304',
         )
         response = client.post('/repository_id/wekwikgene', json=source.model_dump())
@@ -551,7 +536,6 @@ def test_valid_id(self):
     def test_invalid_id(self):
         source = WekWikGeneIdSource(
             id=1,
-            repository_name='wekwikgene',
             repository_id='999999999999999999999999999999',  # Non-existent ID
         )
         response = client.post('/repository_id/wekwikgene', json=source.model_dump())
@@ -562,7 +546,6 @@ def test_invalid_id(self):
     def test_wekwikgene_down(self):
         source = WekWikGeneIdSource(
             id=1,
-            repository_name='wekwikgene',
             repository_id='0000304',
         )
 
@@ -571,12 +554,11 @@ def test_wekwikgene_down(self):
         )
         response = client.post('/repository_id/wekwikgene', json=source.model_dump())
         self.assertEqual(response.status_code, 504)
-        self.assertIn('Unable to connect to wekwikgene', response.json()['detail'])
+        self.assertIn('Unable to connect to WeKwikGene', response.json()['detail'])
 
     def test_redirect(self):
         source = WekWikGeneIdSource(
             id=1,
-            repository_name='wekwikgene',
             repository_id='0000304',
         )
         response = client.post('/repository_id', json=source.model_dump())
@@ -590,7 +572,7 @@ class BenchlingUrlSourceTest(unittest.TestCase):
 
     def test_valid_url(self):
         url = 'https://benchling.com/siverson/f/lib_B94YxDHhQh-cidar-moclo-library/seq_dh1FrJTc-b0015_dh.gb'
-        source = BenchlingUrlSource(id=0, repository_id=url, repository_name='benchling')
+        source = BenchlingUrlSource(id=0, repository_id=url)
         response = client.post('/repository_id/benchling', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
         payload = response.json()
@@ -601,7 +583,7 @@ def test_valid_url(self):
     def test_invalid_url(self):
         # We have to initialize the object with a valid url
         url = 'https://benchling.com/siverson/f/lib_B94YxDHhQh-cidar-moclo-library/seq_dh1FrJTc-b0015_dh.gb'
-        source_object = BenchlingUrlSource(id=0, repository_id=url, repository_name='benchling')
+        source_object = BenchlingUrlSource(id=0, repository_id=url)
 
         # In the dict, we can then edit
         source_dict = source_object.model_dump()
@@ -622,7 +604,7 @@ def test_invalid_url(self):
 
         # One that matches the pattern but does not exist
         url = 'https://benchling.com/bluh/blah.gb'
-        source = BenchlingUrlSource(id=0, repository_id=url, repository_name='benchling')
+        source = BenchlingUrlSource(id=0, repository_id=url)
         response = client.post('/repository_id/benchling', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
         self.assertIn('file requested from url not found', response.json()['detail'])
@@ -632,9 +614,7 @@ class SnapGenePlasmidSourceTest(unittest.TestCase):
 
     def test_valid_url(self):
 
-        source = SnapGenePlasmidSource(
-            id=0, repository_id='basic_cloning_vectors/pEASY-T1_(linearized)', repository_name='snapgene'
-        )
+        source = SnapGenePlasmidSource(id=0, repository_id='basic_cloning_vectors/pEASY-T1_(linearized)')
         response = client.post('/repository_id/snapgene', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
         payload = response.json()
@@ -649,7 +629,6 @@ def test_valid_url(self):
         source2 = SnapGenePlasmidSource(
             id=0,
             repository_id='basic_cloning_vectors/pEASY-T1_(linearized)',
-            repository_name='snapgene',
             output_name='my_name',
         )
         response = client.post('/repository_id/snapgene', json=source2.model_dump())
@@ -661,12 +640,12 @@ def test_valid_url(self):
 
     def test_invalid_url(self):
         # Invalid plasmid set
-        source = SnapGenePlasmidSource(id=0, repository_id='hello/world', repository_name='snapgene')
+        source = SnapGenePlasmidSource(id=0, repository_id='hello/world')
         response = client.post('/repository_id/snapgene', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
 
         # Invalid plasmid name
-        source = SnapGenePlasmidSource(id=0, repository_id='basic_cloning_vectors/hello', repository_name='snapgene')
+        source = SnapGenePlasmidSource(id=0, repository_id='basic_cloning_vectors/hello')
         response = client.post('/repository_id/snapgene', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
         self.assertIn('hello is not part of basic_cloning_vectors', response.json()['detail'])
@@ -681,7 +660,7 @@ def test_invalid_url(self):
 class EuroscarfSourceTest(unittest.TestCase):
 
     def test_valid_url(self):
-        source = EuroscarfSource(id=0, repository_id='P30174', repository_name='euroscarf')
+        source = EuroscarfSource(id=0, repository_id='P30174')
         response = client.post('/repository_id/euroscarf', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
         payload = response.json()
@@ -695,7 +674,7 @@ def test_valid_url(self):
         self.assertTrue(any('yEGFP' in f.qualifiers['gene'] for f in sequence.features))
 
         # Ensure that linear files are circularised
-        source = EuroscarfSource(id=0, repository_id='P30555', repository_name='euroscarf')
+        source = EuroscarfSource(id=0, repository_id='P30555')
         response = client.post('/repository_id/euroscarf', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
         payload = response.json()
@@ -705,7 +684,7 @@ def test_valid_url(self):
 
     def test_invalid_url(self):
         # Compatible with regex, but does not exist
-        source = EuroscarfSource(id=0, repository_id='P99999999999999', repository_name='euroscarf')
+        source = EuroscarfSource(id=0, repository_id='P99999999999999')
         response = client.post('/repository_id/euroscarf', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
 
@@ -718,7 +697,7 @@ def test_invalid_url(self):
     @respx.mock
     def test_circularize_plasmid(self):
         # We mock a request in which we would get a linear plasmid
-        source = EuroscarfSource(id=0, repository_id='P9999999999999', repository_name='euroscarf')
+        source = EuroscarfSource(id=0, repository_id='P9999999999999')
         respx.get('http://www.euroscarf.de/plasmid_details.php').respond(
             200, text='<html><body><a href="files/dna/test.gb">Download</a></body></html>'
         )
@@ -740,21 +719,16 @@ class IGEMSourceTest(unittest.TestCase):
 
     @pytest.mark.flaky(reruns=2, reruns_delay=2)
     def test_igem(self):
-        source = IGEMSource(
-            id=0, repository_name='igem', repository_id='BBa_C0062-pSB1C5C', sequence_file_url=self.good_url
-        )
+        source = IGEMSource(id=0, repository_id='BBa_C0062-pSB1C5C', sequence_file_url=self.good_url)
         response = client.post('/repository_id/igem', json=source.model_dump())
         payload = response.json()
         self.assertEqual(response.status_code, 200)
         self.assertEqual(payload['sources'][0]['repository_id'], 'BBa_C0062-pSB1C5C')
-        self.assertEqual(payload['sources'][0]['repository_name'], 'igem')
 
     def test_errors(self):
 
         # The repository_id does not start with the part_name, even if url is valid
-        source = IGEMSource(
-            id=0, repository_name='igem', repository_id='BBa_C0062-dummy', sequence_file_url=self.good_url
-        )
+        source = IGEMSource(id=0, repository_id='BBa_C0062-dummy', sequence_file_url=self.good_url)
 
         # The url is not a GenBank file
         source_json = source.model_dump()
@@ -763,7 +737,7 @@ def test_errors(self):
         self.assertEqual(response.status_code, 422)
 
         # The url does not exist
-        source = IGEMSource(id=0, repository_name='igem', repository_id='dummy-test', sequence_file_url=self.wrong_url)
+        source = IGEMSource(id=0, repository_id='dummy-test', sequence_file_url=self.wrong_url)
         response = client.post('/repository_id/igem', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
 
@@ -845,9 +819,9 @@ def test_exceptions(self):
 
         # Wrong coordinates
         s = correct_source.model_copy(deep=True)
-        s.start = 1
-        s.end = 10
+        s.coordinates = '1..10'
         response = client.post('/genome_coordinates', json=s.model_dump())
+        self.assertIn('gene should fall within', response.json()['detail'])
         self.assertStatusCode(response.status_code, 400)
         time.sleep(wait_time)
 
@@ -893,7 +867,7 @@ def test_exceptions(self):
         s.locus_tag = None
         s.gene_id = None
         s.assembly_accession = None
-        s.sequence_accession = 'blah'
+        s.repository_id = 'blah'
         response = client.post('/genome_coordinates', json=s.model_dump())
         self.assertStatusCode(response.status_code, 404)
         time.sleep(wait_time)
@@ -902,39 +876,27 @@ def test_exceptions(self):
         viral_source = GenomeCoordinatesSource.model_validate(
             request_examples.genome_region_examples['viral_sequence']['value']
         )
-        viral_source.start = 10
-        viral_source.end = 1
-        response = client.post('/genome_coordinates', json=viral_source.model_dump())
-        self.assertStatusCode(response.status_code, 422)
-        time.sleep(wait_time)
-
-        viral_source.start = 0
-        viral_source.end = 20
+        viral_source.coordinates = '10..1'
         response = client.post('/genome_coordinates', json=viral_source.model_dump())
         self.assertStatusCode(response.status_code, 422)
         time.sleep(wait_time)
 
-        viral_source.start = 1
-        viral_source.end = 20
-        viral_source.strand = 0
+        viral_source.coordinates = '0..20'
         response = client.post('/genome_coordinates', json=viral_source.model_dump())
         self.assertStatusCode(response.status_code, 422)
         time.sleep(wait_time)
 
         # Coordinates outside of the sequence
-        viral_source.start = 1
-        # the length is 2151
-        viral_source.end = 2152
-        viral_source.strand = 1
+        viral_source.coordinates = '1..2152'
         response = client.post('/genome_coordinates', json=viral_source.model_dump())
         self.assertStatusCode(response.status_code, 400)
         time.sleep(wait_time)
 
         # Coordinates too long
-        viral_source.start = 1
-        viral_source.end = 100004
+        viral_source.coordinates = '1..100004'
         response = client.post('/genome_coordinates', json=viral_source.model_dump())
         self.assertStatusCode(response.status_code, 400)
+        self.assertIn('coordinates fall outside the sequence', response.json()['detail'])
 
     def test_ncbi_down(self):
         correct_source = GenomeCoordinatesSource.model_validate(
@@ -948,13 +910,23 @@ def test_ncbi_down(self):
             self.assertEqual(response.status_code, 503)
             self.assertIn('NCBI is down', response.json()['detail'])
 
+    def test_max_sequence_length(self):
+        correct_source = GenomeCoordinatesSource.model_validate(
+            request_examples.genome_region_examples['full']['value']
+        )
+        correct_source.coordinates = f'1..{app_settings.NCBI_MAX_SEQUENCE_LENGTH + 1}'
+        response = client.post('/genome_coordinates', json=correct_source.model_dump())
+        self.assertEqual(response.status_code, 400)
+        self.assertIn(
+            f'sequence is too long (max {app_settings.NCBI_MAX_SEQUENCE_LENGTH} bp)', response.json()['detail']
+        )
+
 
 class SEVASourceTest(unittest.TestCase):
     def test_seva_url(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA261',
-            repository_name='seva',
             sequence_file_url='https://seva-plasmids.com/maps-canonical/maps-plasmids-SEVAs-canonical-versions-web-1-3-gbk/pSEVA261.gbk',
         )
         response = client.post('/repository_id/seva', json=source.model_dump())
@@ -971,7 +943,6 @@ def test_seva_url(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA2a2d1',
-            repository_name='seva',
         )
         response = client.post('/repository_id/seva', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
@@ -980,7 +951,6 @@ def test_ncbi_url(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA2214',
-            repository_name='seva',
             sequence_file_url='https://www.ncbi.nlm.nih.gov/nuccore/MH650998',
         )
         response = client.post('/repository_id/seva', json=source.model_dump())
@@ -997,7 +967,6 @@ def test_errors(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA261',
-            repository_name='seva',
             sequence_file_url='https://seva-plasmids.com/maps-canonical/maps-plasmids-SEVAs-canonical-versions-web-1-3-gbk/pSEVA261.gbk',
         )
 
@@ -1036,14 +1005,14 @@ def test_errors(self):
 
         # Mock connection error
 
-        source = SEVASource(id=0, repository_id='pSEVA261', repository_name='seva')
+        source = SEVASource(id=0, repository_id='pSEVA261')
 
         with respx.mock:
             respx.get(source.sequence_file_url).mock(side_effect=httpx.ConnectError('Mock Error'))
             response = client.post('/repository_id/seva', json=source.model_dump())
             self.assertEqual(response.status_code, 504)
             payload = response.json()
-            self.assertIn('Unable to connect to seva', payload['detail'])
+            self.assertIn('Unable to connect to SEVA', payload['detail'])
 
         # Mock incorrect file
         with respx.mock:
@@ -1066,7 +1035,6 @@ def test_redirect(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA261',
-            repository_name='seva',
             sequence_file_url='https://seva-plasmids.com/maps-canonical/maps-plasmids-SEVAs-canonical-versions-web-1-3-gbk/pSEVA261.gbk',
         )
         with open(f'{test_files}/ase1.gb', 'r') as f:
@@ -1081,7 +1049,6 @@ def test_circularize(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA261',
-            repository_name='seva',
             sequence_file_url='https://seva-plasmids.com/maps-canonical/maps-plasmids-SEVAs-canonical-versions-web-1-3-gbk/pSEVA261.gbk',
         )
         with open(f'{test_files}/ase1.gb', 'r') as f:
@@ -1101,7 +1068,6 @@ def test_valid_url(self):
         source = OpenDNACollectionsSource(
             id=0,
             repository_id='Ecoli Nanobody Toolkit/BC_RJ_SD8',
-            repository_name='open_dna_collections',
         )
         response = client.post('/repository_id/open_dna_collections', json=source.model_dump())
         self.assertEqual(response.status_code, 200)
@@ -1121,7 +1087,6 @@ def test_errors(self):
         source = OpenDNACollectionsSource(
             id=0,
             repository_id='Ecoli Nanobody Toolkit/BC_RJ_SD8',
-            repository_name='open_dna_collections',
             sequence_file_url='https://assets.opencloning.org/open-dna-collections/Ecoli%20Nanobody%20Toolkit/genbank_seq/hello.txt',
         )
         response = client.post('/repository_id/open_dna_collections', json=source.model_dump())
@@ -1130,7 +1095,6 @@ def test_errors(self):
         source = OpenDNACollectionsSource(
             id=0,
             repository_id='hello/BC_RJ_SD8',
-            repository_name='open_dna_collections',
         )
         response = client.post('/repository_id/open_dna_collections', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
@@ -1139,7 +1103,6 @@ def test_errors(self):
         source = OpenDNACollectionsSource(
             id=0,
             repository_id='Ecoli Nanobody Toolkit/hello',
-            repository_name='open_dna_collections',
         )
         response = client.post('/repository_id/open_dna_collections', json=source.model_dump())
         self.assertEqual(response.status_code, 404)
@@ -1159,7 +1122,6 @@ def test_not_allowed_external_url(self):
         source = SEVASource(
             id=0,
             repository_id='pSEVA261',
-            repository_name='seva',
             sequence_file_url='https://seva-plasmids.com/dummy.gbk',
         )
         response = client.post('/repository_id/seva', json=source.model_dump())
diff --git a/tests/test_endpoints_no_input.py b/tests/test_endpoints_no_input.py
index 13bcd1fa..8557859c 100644
--- a/tests/test_endpoints_no_input.py
+++ b/tests/test_endpoints_no_input.py
@@ -11,6 +11,7 @@
     TextFileSequence,
     ManuallyTypedSource,
     OligoHybridizationSource,
+    ManuallyTypedSequence,
 )
 
 
@@ -96,10 +97,11 @@ def test_manually_typed(self):
         # Test linear (default)
         source = ManuallyTypedSource(
             id=0,
-            user_input='ATGC',
         )
+        sequence = ManuallyTypedSequence(id=0, sequence='ATGC')
+        data = {'source': source.model_dump(), 'sequence': sequence.model_dump()}
 
-        response = client.post('/manually_typed', json=source.model_dump())
+        response = client.post('/manually_typed', json=data)
         self.assertEqual(response.status_code, 200)
         payload = response.json()
         resulting_sequences = [
@@ -113,8 +115,8 @@ def test_manually_typed(self):
         self.assertEqual(sources[0], source)
 
         # Test circular
-        source.circular = True
-        response = client.post('/manually_typed', json=source.model_dump())
+        data['sequence']['circular'] = True
+        response = client.post('/manually_typed', json=data)
         self.assertEqual(response.status_code, 200)
         payload = response.json()
         resulting_sequences = [
@@ -131,12 +133,11 @@ def test_manually_typed(self):
         # Test overhangs
         source = ManuallyTypedSource(
             id=0,
-            user_input='ATGC',
-            overhang_crick_3prime=1,
-            overhang_watson_3prime=2,
         )
+        sequence = ManuallyTypedSequence(id=0, sequence='ATGC', overhang_crick_3prime=1, overhang_watson_3prime=2)
+        data = {'source': source.model_dump(), 'sequence': sequence.model_dump()}
 
-        response = client.post('/manually_typed', json=source.model_dump())
+        response = client.post('/manually_typed', json=data)
         self.assertEqual(response.status_code, 200)
         payload = response.json()
         resulting_sequences = [
@@ -147,17 +148,19 @@ def test_manually_typed(self):
         self.assertEqual(resulting_sequences[0].seq, Dseq.from_full_sequence_and_overhangs('ATGC', 1, 2))
 
         # Test that if overhangs are set, it cannot be circular
-        wrong_source = source.model_dump()
-        wrong_source['circular'] = True
+        wrong_data = data.copy()
+        wrong_data['sequence']['circular'] = True
 
-        response = client.post('/manually_typed', json=wrong_source)
+        response = client.post('/manually_typed', json=wrong_data)
         self.assertEqual(response.status_code, 422)
 
     # Test that it fails if not acgt or empty
     def test_manually_typed_fail(self):
 
-        response = client.post('/manually_typed', json={'user_input': 'ATGZ'})
+        response = client.post(
+            '/manually_typed', json={'source': {'id': 0}, 'sequence': {'id': 0, 'sequence': 'ATGZ'}}
+        )
         self.assertEqual(response.status_code, 422)
 
-        response = client.post('/manually_typed', json={'user_input': ''})
+        response = client.post('/manually_typed', json={'source': {'id': 0}, 'sequence': {'id': 0, 'sequence': ''}})
         self.assertEqual(response.status_code, 422)
diff --git a/tests/test_files/bug_fixing/digestion_spanning_origin.json b/tests/test_files/bug_fixing/digestion_spanning_origin.json
index b10689f4..6863fd51 100644
--- a/tests/test_files/bug_fixing/digestion_spanning_origin.json
+++ b/tests/test_files/bug_fixing/digestion_spanning_origin.json
@@ -31,22 +31,14 @@
       "type": "ManuallyTypedSource",
       "output_name": null,
       "database_id": null,
-      "input": [],
-      "overhang_crick_3prime": 0,
-      "overhang_watson_3prime": 0,
-      "user_input": "TTCaaaaGAA",
-      "circular": true
+      "input": []
     },
     {
       "id": 2,
       "type": "ManuallyTypedSource",
       "output_name": null,
       "database_id": null,
-      "input": [],
-      "overhang_crick_3prime": 0,
-      "overhang_watson_3prime": 0,
-      "user_input": "ttcccccccgaa",
-      "circular": true
+      "input": []
     },
     {
       "id": 3,
@@ -78,7 +70,7 @@
   "primers": [],
   "description": "",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/bug_fixing/example_error_assembly_origin_spanning_feature.json b/tests/test_files/bug_fixing/example_error_assembly_origin_spanning_feature.json
index 3664a9d1..5874becf 100644
--- a/tests/test_files/bug_fixing/example_error_assembly_origin_spanning_feature.json
+++ b/tests/test_files/bug_fixing/example_error_assembly_origin_spanning_feature.json
@@ -133,7 +133,7 @@
   "primers": [],
   "description": "",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/bug_fixing/gateway_13bp_followed_by_digestion.json b/tests/test_files/bug_fixing/gateway_13bp_followed_by_digestion.json
index 412ff6e0..722d8971 100644
--- a/tests/test_files/bug_fixing/gateway_13bp_followed_by_digestion.json
+++ b/tests/test_files/bug_fixing/gateway_13bp_followed_by_digestion.json
@@ -56,13 +56,11 @@
       "output_name": null,
       "database_id": null,
       "input": [],
+      "repository_id": "NC_000913.3",
+      "coordinates": "complement(362231..367305)",
       "assembly_accession": "GCF_000005845.2",
-      "sequence_accession": "NC_000913.3",
       "locus_tag": "b0344",
-      "gene_id": 945006,
-      "start": 362231,
-      "end": 367305,
-      "strand": -1
+      "gene_id": 945006
     },
     {
       "id": 2,
@@ -70,8 +68,7 @@
       "output_name": "pDONR221",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pDONR221",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pDONR221"
     },
     {
       "id": 3,
@@ -79,8 +76,7 @@
       "output_name": "pcDNA6.2_C-YFP-DEST",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pcDNA6.2_C-YFP-DEST",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pcDNA6.2_C-YFP-DEST"
     },
     {
       "id": 4,
@@ -197,7 +193,7 @@
   ],
   "description": "Cloning the lacZ gene from E. coli into an entry clone, then expression clone",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/bug_fixing/gateway_13bp_overlap.json b/tests/test_files/bug_fixing/gateway_13bp_overlap.json
index cc3f78c4..b7f2ed91 100644
--- a/tests/test_files/bug_fixing/gateway_13bp_overlap.json
+++ b/tests/test_files/bug_fixing/gateway_13bp_overlap.json
@@ -56,13 +56,11 @@
       "output_name": null,
       "database_id": null,
       "input": [],
+      "repository_id": "NC_000913.3",
+      "coordinates": "complement(362231..367305)",
       "assembly_accession": "GCF_000005845.2",
-      "sequence_accession": "NC_000913.3",
       "locus_tag": "b0344",
-      "gene_id": 945006,
-      "start": 362231,
-      "end": 367305,
-      "strand": -1
+      "gene_id": 945006
     },
     {
       "id": 2,
@@ -70,8 +68,7 @@
       "output_name": "pDONR221",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pDONR221",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pDONR221"
     },
     {
       "id": 3,
@@ -79,8 +76,7 @@
       "output_name": "pcDNA6.2_C-YFP-DEST",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pcDNA6.2_C-YFP-DEST",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pcDNA6.2_C-YFP-DEST"
     },
     {
       "id": 4,
@@ -196,7 +192,7 @@
   ],
   "description": "Cloning the lacZ gene from E. coli into an entry clone, then expression clone",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/bug_fixing/gateway_correct.json b/tests/test_files/bug_fixing/gateway_correct.json
index 40015cf2..57647ca4 100644
--- a/tests/test_files/bug_fixing/gateway_correct.json
+++ b/tests/test_files/bug_fixing/gateway_correct.json
@@ -40,13 +40,11 @@
       "output_name": null,
       "database_id": null,
       "input": [],
+      "repository_id": "NC_000913.3",
+      "coordinates": "complement(362231..367305)",
       "assembly_accession": "GCF_000005845.2",
-      "sequence_accession": "NC_000913.3",
       "locus_tag": "b0344",
-      "gene_id": 945006,
-      "start": 362231,
-      "end": 367305,
-      "strand": -1
+      "gene_id": 945006
     },
     {
       "id": 2,
@@ -54,8 +52,7 @@
       "output_name": "pDONR221",
       "database_id": null,
       "input": [],
-      "repository_id": "gateway_cloning_vectors/pDONR221",
-      "repository_name": "snapgene"
+      "repository_id": "gateway_cloning_vectors/pDONR221"
     },
     {
       "id": 3,
@@ -146,7 +143,7 @@
   ],
   "description": "Cloning the lacZ gene from E. coli into an entry clone, then expression clone",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": "0.2.8.3.post7.dev0+e39da02",
   "frontend_version": "v0.2.12.8-4-g30b2f82"
 }
diff --git a/tests/test_files/bug_fixing/homologous_recombination.json b/tests/test_files/bug_fixing/homologous_recombination.json
index a31388b7..d405efc9 100644
--- a/tests/test_files/bug_fixing/homologous_recombination.json
+++ b/tests/test_files/bug_fixing/homologous_recombination.json
@@ -41,7 +41,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "19342",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/8997/a6b027f8-013a-4b68-bf7e-359f34a653d0/addgene-plasmid-19342-sequence-8997.gbk",
       "addgene_sequence_type": "depositor-full"
     },
@@ -82,13 +81,11 @@
       "output_name": null,
       "database_id": null,
       "input": [],
+      "repository_id": "CU329670.1",
+      "coordinates": "1877189..1881726",
       "assembly_accession": "GCA_000002945.3",
-      "sequence_accession": "CU329670.1",
       "locus_tag": "SPOM_SPAPB1A10.09",
-      "gene_id": null,
-      "start": 1877189,
-      "end": 1881726,
-      "strand": 1
+      "gene_id": null
     },
     {
       "id": 4,
@@ -139,7 +136,7 @@
   ],
   "description": "Deletion of the ORF of ase1 by homologous recombination in S.pombe",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/bug_fixing/pcr_spanning_origin.json b/tests/test_files/bug_fixing/pcr_spanning_origin.json
index fbfa442b..75272e04 100644
--- a/tests/test_files/bug_fixing/pcr_spanning_origin.json
+++ b/tests/test_files/bug_fixing/pcr_spanning_origin.json
@@ -23,11 +23,7 @@
       "type": "ManuallyTypedSource",
       "output_name": null,
       "database_id": null,
-      "input": [],
-      "overhang_crick_3prime": 0,
-      "overhang_watson_3prime": 0,
-      "user_input": "ATGCAAACAGTAATGATGGATGACATTCAAAGCACTGATTCTATTGCTGAAAAAGATAATCACTCTAATAATGAATCTAACTTTACTTG",
-      "circular": true
+      "input": []
     },
     {
       "id": 2,
@@ -79,7 +75,7 @@
   ],
   "description": "",
   "files": null,
-  "schema_version": "0.4.3",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_files/homologous_recombination.json b/tests/test_files/homologous_recombination.json
index 1f4c8a5e..d405efc9 100644
--- a/tests/test_files/homologous_recombination.json
+++ b/tests/test_files/homologous_recombination.json
@@ -41,7 +41,6 @@
       "database_id": null,
       "input": [],
       "repository_id": "19342",
-      "repository_name": "addgene",
       "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/8997/a6b027f8-013a-4b68-bf7e-359f34a653d0/addgene-plasmid-19342-sequence-8997.gbk",
       "addgene_sequence_type": "depositor-full"
     },
@@ -82,13 +81,11 @@
       "output_name": null,
       "database_id": null,
       "input": [],
+      "repository_id": "CU329670.1",
+      "coordinates": "1877189..1881726",
       "assembly_accession": "GCA_000002945.3",
-      "sequence_accession": "CU329670.1",
       "locus_tag": "SPOM_SPAPB1A10.09",
-      "gene_id": null,
-      "start": 1877189,
-      "end": 1881726,
-      "strand": 1
+      "gene_id": null
     },
     {
       "id": 4,
@@ -139,7 +136,7 @@
   ],
   "description": "Deletion of the ORF of ase1 by homologous recombination in S.pombe",
   "files": null,
-  "schema_version": "0.4.7",
+  "schema_version": "0.4.9",
   "backend_version": null,
   "frontend_version": null
 }
diff --git a/tests/test_ncbi_requests.py b/tests/test_ncbi_requests.py
index 69387517..8f62905e 100644
--- a/tests/test_ncbi_requests.py
+++ b/tests/test_ncbi_requests.py
@@ -8,6 +8,8 @@
 from fastapi import HTTPException
 import unittest
 
+from Bio.SeqFeature import SimpleLocation
+
 
 class NcbiAsyncRequestsTest(unittest.IsolatedAsyncioTestCase):
 
@@ -95,11 +97,9 @@ async def test_get_genome_region_from_annotation(self):
         seq = await ncbi_requests.get_genome_region_from_annotation(annotation, 1000, 1000)
         self.assertEqual(seq.source.locus_tag, 'YDR294C')
         self.assertEqual(seq.source.gene_id, 851888)
-        self.assertEqual(seq.source.sequence_accession, 'NC_001136.10')
+        self.assertEqual(seq.source.repository_id, 'NC_001136.10')
         self.assertEqual(seq.source.assembly_accession, 'GCF_000146045.2')
-        self.assertEqual(seq.source.start, 1049459)
-        self.assertEqual(seq.source.end, 1053228)
-        self.assertEqual(seq.source.strand, -1)
+        self.assertEqual(seq.source.coordinates, SimpleLocation(1049458, 1053228, -1))
         self.assertEqual(len(seq), 3770)
 
     async def test_get_info_from_annotation(self):
@@ -170,3 +170,8 @@ async def test_get_info_from_annotation(self):
         )
         self.assertEqual(gene_id, None)
         self.assertEqual(locus_tag, None)
+
+    async def test_get_genbank_sequence_errors(self):
+        with pytest.raises(ValueError) as e:
+            await ncbi_requests.get_genbank_sequence('NC_003424.3', None, 10, 1)
+        assert e.value.args[0] == 'start, end, and strand must either all be None or none be None'
diff --git a/tests/test_stub_route.py b/tests/test_stub_route.py
index c12e3353..7d24c404 100644
--- a/tests/test_stub_route.py
+++ b/tests/test_stub_route.py
@@ -2,7 +2,7 @@
 import unittest
 import shutil
 import os
-from opencloning_linkml.datamodel import ManuallyTypedSource, RestrictionEnzymeDigestionSource
+from opencloning_linkml.datamodel import ManuallyTypedSource, RestrictionEnzymeDigestionSource, ManuallyTypedSequence
 from pytest import MonkeyPatch
 from importlib import reload
 from pydna.dseqrecord import Dseqrecord
@@ -43,12 +43,11 @@ def tearDown(self):
         reload(main)
 
     def test_stub_route(self):
-        source = ManuallyTypedSource(
-            id=0,
-            user_input='ATGC',
-        )
+        source = ManuallyTypedSource(id=0)
+        sequence = ManuallyTypedSequence(id=0, sequence='ATGC')
+        data = {'source': source.model_dump(), 'sequence': sequence.model_dump()}
 
-        response = self.client.post('/manually_typed', json=source.model_dump())
+        response = self.client.post('/manually_typed', json=data)
         self.assertEqual(response.status_code, 200)
 
         self.assertTrue(os.path.exists('stubs/manually_typed/'))