Words similar to hmmer

Example sentences for: hmmer

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Alignment of the query sequence is done programs from the HMMER package http://hmmer.wustl.edu/.
1. Query sequence Q is aligned to the existing alignment A (using hmmalign from the HMMER package and the Pfam profile HMM H ).
2. Run hmmbuild -o A' on A , using the same options as were used to build the original Pfam HMM for A , resulting in alignment A' . (HMMER's construction procedure slightly modifies the input alignment in ways that are usually unimportant, but which matter to bootstrapping in RIO.)
We use the Pfam protein family database [ 8 ] as a source of high quality curated multiple sequence alignments and profile HMMs (Hidden Markov Models, see [ 21 ] for a review), as well as programs from the HMMER package http://hmmer.wustl.edu/.
A curated multiple alignment A from the Pfam database for the protein family that Q belongs to (as determined by hmmpfam from the HMMER package).