sokrypton / sokrypton/ColabFold
Accession numbers for MSA
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Description
Hi!
I am currently exploring the behaviour of ColabFold with different custom MSAs and was hoping to explore which sequences are ending up in the MMSeqs MSAs a little more closely. After unpickling the msa.pickle file that ColabFold_advanced outputs, I only see a dictionary with entries for "msas" and "deletion_matrices".
- Is this the expected behaviour?
- If so, is there any way of getting the program to also output accession numbers/DB IDs for the sequences in the MMSeqs MSA.
Apologies if this has been addressed elsewhere.
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 inspecting the unpickled msa.pickle output from ColabFold_advanced and tracing how the MMSeqs MSAs are produced. Determine whether accession numbers or database IDs are retained, then define completion as either documenting the expected dictionary contents or exposing those identifiers alongside the sequences.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 32/100