HH-suite custom db with precomputed MSA

Question

[mnsp088]

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: https://github.com/soedinglab/hh-suite/wiki#building-customized-databases 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.

[Joe]

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.

[mnsp088]

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?

[Joe]

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!