griffithlab / griffithlab/pVACtools
Add reference proteome Blast step to pVACvector
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- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
When running with an input fasta we would blast each fasta sequence.
In cases where the input is a pVACseq list of epitopes (+ VCF), we need to further discuss which sequence to blast. If blasting larger sequence for each epitopes we would almost certainly get false-positive hits to the reference proteome around the mutation position.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the pVACvector workflow for input FASTA files and its existing BLAST handling. Compare that with the pVACseq epitope-list plus VCF path, then clarify which sequence should be searched and how mutation-region false positives will be avoided. Done requires an agreed reference-proteome BLAST design for both input cases.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100