Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
decode protein-lncRNA, protein-ncRNA, protein-mRNA interactions from CLIP-Seq data yjhua2110 RNA Sequencing 9 06-04-2015 01:12 AM
Question: Searching FASTA file for specific IDs aw90 Bioinformatics 1 07-19-2013 04:14 AM
trimming FASTA file baika Bioinformatics 7 03-05-2013 11:03 AM
Convert WIG file into Fasta file kumardeep Bioinformatics 3 08-23-2012 05:56 AM
Searching for substitutions in a VCF file Rubal7 Bioinformatics 0 02-07-2012 11:03 AM

Thread Tools
Old 10-13-2014, 04:37 AM   #1
Location: UK

Join Date: Feb 2014
Posts: 60
Default Searching for protein in fasta file

So I have protein (cas1) I want to look for in a bunch of fasta files and Pfam has a 'HMM logo' for the protein ( I was wondering if it is possible to download the HMM profile from Pfam and use that to look through my files to identify if the protein is present or not?

If not then does anyone have a suggestion of how I could go about looking for this protein in fasta files?
thh32 is offline   Reply With Quote
Old 10-21-2014, 12:16 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Yes, you can download the PFAM model and the HMMER3 software to run the search locally. This is the same tool used for making the PFAM database and running the PFAM search on their website.
maubp is offline   Reply With Quote

crispr, pfam, protein

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:32 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO