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biocore / microprot

structural annotation pipeline for microbial genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
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Uniclust and Uniboost performance on contact predictions #24

Closed tkosciol closed 4 years ago

tkosciol commented 7 years ago

Once the pipeline is ready, test the performance of HHblits MSAs with UniClust30 and UniBoost10/20/30 databases on contact predictions. Use a reference set of easy (PSICOV set) and hard (CASP11 set) targets to evaluate.

tkosciol commented 7 years ago

I don't think that's feasible to assess given the time it might take to convert UniBoost to UniBoost_hhsuite (not available on http://gwdu111.gwdg.de/~compbiol/uniclust/2017_04/)

tkosciol commented 7 years ago

@bctaylor maybe you'd be willing to look into this at some point? Reference data is here: https://uniclust.mmseqs.com and I'd recommend looking into the paper mentioned on the website.

HHsuite is installed on Barnacle in /projects/microprot/tools/hh-suite-3.0.0/build

It's not urgent, but it would be interesting to see if that's feasible and do we see any changes in performance.

tkosciol commented 4 years ago

obsolete with the release of the BigFatDB