Problems about human germline sequence
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- Dominant language
- Python
- Stars
- 265
- Forks
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Description
While using humanization module at https://biophi.dichlab.org/, I found the sequence of IGKV2-30*01 was different from the sequence from http://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-AA-WithoutGaps-F+ORF+inframeP .The second sequence was copied from the biophi web page.
Maybe there are some errors with your human germline V and J gene sequences.
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the discrepancy for IGKV2-30*01 in the BioPhi humanization module and compare it with the IMGT reference FASTA linked in the report. Trace which germline V and J gene sequence source the module uses; done means identifying whether the mismatch is an error and correcting or documenting the source discrepancy with regression coverage.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100