Faking hh-suite workflow / alignment output

Faking hh-suite workflow / alignment output

1

Given the following:

  • query.fasta -> single entry
  • reference.fasta -> multiple entries

I now want to ‘fake’ (or just be able to get) an output that looks like a proper *.hhr alignment file, i.e. as if I aligned the query.fasta against the profiles of the sequences in the reference.fasta. I think this can be achieved with

hhsearch -i query.fasta -d reference.ff{data,index}

However, i really don’t want the extra steps from aligning the reference sequences to any DB and all that HMM building. I am just interested in aligning the query against the reference sequences and then getting the same format in .hhr file (ordering, alignments, statistics).

I cannot figure out how to do that. Everything in hhsuite feels very long-winded.

For a single sequence in the reference.fasta hhalign does the job. To clarify, the sequences in reference.fasta might have some similarities but they also might be very different. Doing an MSA first on these doesnt make much sense. I am probably missing something super obvious but I cannot figure out how to get to this .hhr file of indepedant sequence sin the reference.fasta.-

Thanks!


alignment


hhsuite

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