protein motif search software

[jwhite]

Hello,

Can anyone suggest a software application that will search for motifs in amino acid sequence (FASTA files)? I have about a 100 files that I need to scan for motifs. This could be done online as well, since a suitable motif database is also necessary.

I'd prefer an application that I can set up on our cluster, but don't know which software works best.

Joe White

[rhinoceros]

HMMER3 on Pfam A

[jwhite]

HMMER3 on Pfam A

Thanks. HMMER3 does full sequence searches. What I'm looking for are motifs within sequences, eg. signal sequences, SH3 domains, etc. I suppose it depends on the database used for the search, so an amino acid motif database would be most useful.

Joe White

[rhinoceros]

Thanks. HMMER3 does full sequence searches. What I'm looking for are motifs within sequences, eg. signal sequences, SH3 domains, etc. I suppose it depends on the database used for the search, so an amino acid motif database would be most useful.

Joe White

No, HMMER3 on Pfam A is exactly what you want. Check the manual. Here's for example SH3 Pfam.

[jwhite]

No, HMMER3 on Pfam A is exactly what you want. Check the manual. Here's for example SH3 Pfam.

Thanks for your help.
Joe