biocore / biocore/microprot

auto build and update microprot_db and HH-suite compatible DB

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version 3
Dominant language
Python
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2
Forks
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Description

Databases which we build from publicly available and in-house genomic and metagenomic data need to be updatable and we need to generate scripts to automatically generate updates for HH-suite compatible DB.

We need it for the last part of the pipeline `MSA_hhblits` where we search against UniClust30 and (after this issue is resolved) against our `microprot_db`.

Building the seed `microprot_db` is done, now we need to write a script to automatically update current clustering using `mmseqs` and find an effective way to create HH-suite databases from those updated clusterings.

*References:*
MMseqs: https://github.com/soedinglab/mmseqs2/wiki#updating-a-database-clustering-using-mmseqs-clusterupdate
UniClust pipeline (building HHsuite DB): https://github.com/soedinglab/uniclust-pipeline/blob/master/run_hhdatabase.sh
HHsuite (section 4.9): https://github.com/soedinglab/hh-suite/blob/master/hhsuite-userguide.pdf

I've got some preliminary scripts. If interested, please inquire offline.

Contributor guide

No contributing guide indexed for this repository

Research direction

No repository files or tests are identified. Start at the MSA_hhblits pipeline stage, then review the MMseqs clusterupdate reference, UniClust's run_hhdatabase.sh, and HH-suite guide section 4.9. Done means an automated process updates the current microprot_db clustering and produces an HH-suite-compatible database for pipeline searches.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data-engineering, databases
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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