hmmer and pfam

[rhinoceros]

Could somebody explain to me briefly how to use Pfam's hmm with hmmer.

For example, what are the steps for using the file from this site (raw hmm) with hmmalign?

hmmalign -o output thefile.hmm myseqs.fasta

Doesn't produce any errors. However, it's no alignment. All the sequences are still in the same exact order as they were in myseqs.fasta

[Apexy]

Hi,
I noticed your query has note attended to. Let me attempt a learners non-specialist answer. if I remember well, there are a number of executables in the hmmer package to achieve different things. What do you plan to achieve with hmmer?
For example, the only thing I remember is to acribe functional lable to sequences in a FASTA file. I evoked hmmer like so:
hmmscan --domtblout test.tab --cut_ga --acc --cpu 10 Pfam-A.hmm test.fa

where test.tab is the output in tabular format.

Hope this helps you one step into your task.

cheers

[rhinoceros]

I think I figured it out. There's nothing wrong with my output. hmmalign doesn't align sequences (vs sequences), more like, it aligns sequences to a hmm. Thus, the order of the sequences in the alignment is meaningless (and subsequently the same than in the input file).