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Old 03-22-2014, 07:11 AM   #1
grem
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Location: Boston

Join Date: Oct 2013
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Question trying to understand pfams

I want to download seqs of a pfam, build an hmm, and search a genome for the hmm.

The wellcome sanger site is a bit confusing to me. I can see there are 250 or so sequences total in the pfam, but it also says there are 4 different architectures. What does this mean? 4 "types" in this pfam? Does this mean I want to hmm search 4 times? Which sequences map to which architectures?

Any help appreciated.
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Old 03-25-2014, 12:28 AM   #2
gprakhar
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The hmmer tool, is your best bet for searching a nucleotide sequence with a hmm model.
For a detailed appreciation of hmm model use and lot of examples please refer to the
hmmer 3 documentation

hope this helps,
--
pg
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