This is a test version of Biostars. For the public version, visit https://www.biostars.org.
ECOD HHMdb to hh-suite

Hello, do you know how I am suppose to make HH-suite database from ecod.latest.F99.hhm_db from:

http://prodata.swmed.edu/ecod/complete/distribution

hhsuite databases have many other files: a3m.ffdata, a3m.ffindex etc.

do you know how to solve this?

Best,

X

edit: I found this now: https://github.com/soedinglab/hh-suite/wiki#building-customized-databases but still I am confused

hhm hh-suite hhpred
• 1,659 views • link
updated by Mensur Dlakic Mensur Dlakic • written by Xylanaser Xylanaser

1 answer

Those files will work only with v2.0.15 of the HH-suite. They are simple concatenations of individual HHMs that can be used with hhsearch from the above-mentioned version. Either ask ECOD authors to make those files for HH-suite v3.xx, or you will have to use the older version. Alternatively, you can try building the v3.xx indexed database from the alignments provided on ECOD site (using Wiki instructions), though I am not sure if those are the same alignments that were used to build HHMs.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thank you for answer :)

• 0 views • link
written by Xylanaser Xylanaser

Log in to answer this question.

More posts like this