Question: HH-suite custom db with precomputed MSA
gravatar for mnsp088
6 months ago by
mnsp08840 wrote:

Hi everyone. I am trying to create a custom database in HH-suite using a precomputed multiple sequence alignment (MSA) that I got from MUSCLE. I'm following the steps outlined here: and I skipped to making the HMM model step (since I already have my MSA), however the ffindex_apply_mpi module requires two input files: input data and index file. I'm using the output from MUSCLE (fa.out file) as the input data but does anyone know where I can get the index file from?

> ffindex_apply_mpi <db>_a3m.ff{data,index} \\
>     -i <db>_hhm.ffindex -d <db>_hhm.ffdata -- hhmake -i stdin -o stdout -v 0

thank you.

msa hmm hh-suite • 363 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by mnsp08840

AFAIK, you're making the index in this step:

First of all we split the concatenated fasta file to an ffindex with ffindex_from_fasta.

ffindex_from_fasta -s <db>_fas.ff{data,index} <db.fas>

The index file should be the .ffindex if I've understood those instructions correctly.

ADD REPLYlink modified 6 months ago • written 6 months ago by Joe15k

I thought ffindex_from_fasta creates the files to be used to make the MSA using hhblits and their uniclust db:

hhblits_mpi -i <db>_fas -d <path_to uniclust30=""> -oa3m <db>_a3m_wo_ss -n 2 -cpu 1 -v 0

but since I already have a precomputed MSA I skipped these steps and tried to build the HMM profile directly. Is this possible?

ADD REPLYlink modified 6 months ago • written 6 months ago by mnsp08840

Ah on closer reading I see you might be right. Looking at those instructions there doesn't appear to be an alternative, but I can't say for sure. I've used hhsuite extensively, but never tried to use a custom DB, so I'll have to bow out to someone who knows better!

ADD REPLYlink written 6 months ago by Joe15k
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