Entering edit mode
3.1 years ago
usr2
▴
10
hmmsearch manual specifies:
"hmmsearch is used to search one or more profiles against a sequence database"
However I could not find specification about how to specify multiple queries. I tried hmmsearch [options] <hmmfile1> <hmmfile> <seqdb> without succes.
Does someone know if its possible to search for proteins with two profiles?
thanks & cheers,
Many thanks! :)
how can we download seqdb file
You can use any appropriate multi-fasta sequence file.
I have one protein fa file. Now how can I convert that file into seqdb?
For hmmsearch, I wrote one command line once please check and let me know what's wrong in it hmmsearch --tblout <profile_PF03936.hmm> GCF_907164915.1_protein.faa > search_PF03936
No conversion is needed.
Here is a basic example courtesy of GPT. You need to have these minimum options.
You should not be literal with the example command I gave. Left and right single angle characters in the example above signify that the name inside is generic, and should be replaced with your own appropriate file name. For your example it most likely should be:
This will use a HMM file
profile_PF03936.hmm
, a sequence fileGCF_907164915.1_protein.faa
and save tabular output intable_out.txt
and the screen output insearch_PF03936
. That means you didn't provide a name for the table output and HMM name should not be in single angle brackets.