Question: hmmscan using Pfam databases
0
gravatar for dimitrischat
8 months ago by
dimitrischat120
dimitrischat120 wrote:

Hello,

wanted to ask if you could do a specific search using pfam databases, f.e. plants ( taxid: 33090 )?

Thanks

hmmscan --cpu 8 --domtblout pfam.domtblout /path/to/Pfam-A.hmm transdecoder_dir/longest_orfs.pep

edit: or maybe i could edit the database Pfam-A.hmm and keep only taxonomy 33090 (viridiplantae) ?

rna-seq • 341 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by dimitrischat120

Could you elaborate on your question?

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https://saf.bio.caltech.edu/saf_manuals/hmmer/v2_3_2.pdf

ADD REPLYlink written 8 months ago by Fatima630
1
gravatar for h.mon
8 months ago by
h.mon31k
Brazil
h.mon31k wrote:

Go to the Pfam search page, select the taxonomy tab, enter Viridiplantae as query term and toggle the Find domains unique to query term box. It should return Viridiplantae-specific domains, but I am unable to confirm, as I get the following message:

There was a system error on your last request.

This error has been recorded and will be investigated. If you would like to let us know what you were doing when the error occurred, please file a bug report.

You might like to go back to the previous page and see if it works this time...

I don't know if this is a temporary issue, a bug or some error from my part. I tried the above search strategy with Viridiplantae, Embryophyta, Tracheophyta, Spermatophyta, all produced the same error message. You may try contacting Pfam to further investigate the issue. If one does not select the Find domains unique to query term box, the search does indeed returns results - but this is not what you want.

edit: as Pfam is organized in terms of protein domains, it may well be there is no domain exclusive to the above search terms. If this is the case, the Pfam error message could be improved.

ADD COMMENTlink modified 8 months ago • written 8 months ago by h.mon31k

Thanks a lot for your help. Unfortunately i get the same error when toggling the "..unique.." option. I contacted them via email, hope they reply.

ADD REPLYlink written 8 months ago by dimitrischat120

what do you mean by that "as Pfam is organized in terms of protein domains, it may well be there is no domain exclusive to the above search terms. If this is the case, the Pfam error message could be improved." ?

ADD REPLYlink written 8 months ago by dimitrischat120
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