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Example sentences for: hmmer

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Alignment of the query sequence is done programs from the HMMER package http://hmmer.wustl.edu/.
In contrast, analyses using profile search algorithms such as HMMER http://hmmer.wustl.edu/and Pfam [ 8 ] classify sequences too generally.
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/.
Sequence-profile methods such as PSI-BLAST [ 1 ] or HMMER [ 2 ] are often used to detect distant homologs, and resources such as Prosite [ 3 ] , BLOCKS [ 4 ] and PFAM [ 5 ] are representative resources resulting from protein classification based on sequence patterns.