sokrypton / sokrypton/ColabFold
How to find MSA coverage
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Description
The coverage shown in the MSA plots seems different to the output .a3m file. For example for PDB ID 9PAI, the coverage plot is:
But the number of sequences in the 9PAI.a3m file is ~22000. What is the root cause of this discrepancy?
Contributor guide
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 comparing the coverage plot for PDB ID 9PAI with the sequence count in 9PAI.a3m, then trace how each value is calculated or reported. The issue is resolved when the root cause of the discrepancy is documented and the expected relationship between plot coverage and alignment sequences is clear.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100