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Old 10-13-2014, 04:37 AM   #1
thh32
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Location: UK

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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 (http://pfam.xfam.org/family/PF01867#tabview=tab4). 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?
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Old 10-21-2014, 12:16 AM   #2
maubp
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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.
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