Improve ORF coordinates detection
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enhancement
- Dominant language
- Python
- Stars
- 5
- Forks
- 4
- Avg merge
- 10h 7m
- Merged PRs (30d)
- 5
Description
Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.
The searched subtype ORF sequence should be prefixed and suffixed with "+" to discourage spread of nucleotides.
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 locating the ORF coordinate detection entry point and the current whole-genome alignment logic. Trace how the searched subtype ORF and full query sequence are passed into alignment, then verify that the ORF is prefixed and suffixed with "+" and that coordinates are detected from the targeted alignment rather than a whole-genome alignment.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100