(hmmsearch) find targets with multiple query profiles with hmmsearch

Question

[usr2]

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,

Answer 1

[Mensur Dlakic]

You will have to concatenate multiple HMMs into a single file. They have a double slash // to signify the end of profile, and the program knows that whatever comes next will be a separate profile. After that, you do a simple command:

hmmsearch [options] <concatenated_hmmfile> <seqdb>

[usr2]

Many thanks! :)