Pfam and HMMER We have already mentioned the Pfam database as a source of multiple alignments for more than 2400 protein domain families. But what really makes Pfam useful is its tight relationship with a program package that implements hidden Markov models:HMMER , which is written by Sean Eddy. The Pfam multiple alignments have been used to build HMMs for each and every protein domain family. Using one of the programs in the HMMER package, it is possible to search for the presence of a known domain in a sequence of your own. The web sites for Pfam all have facilities to do this via the Web. This is very useful, and the web sites contains several different tools and search possibilities. However, if one wishes to work on a multiple alignment of ones own, and use that for searches, one must download the HMMER package and set it up, which is pretty straightforward. The HMMER package contains several different programs: • hmmalign: Align a sequence to a given HMM profile. • hmmbuild: build a profile HMM from an alignment.
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