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Example sentences for: hmmer

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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 searches were carried out using the PSI-BLAST program, with the cut-off for inclusion of sequences into the profile set at E = 0.01 [ 3, 9], and the HMMer program package [ 57].
This requires specially prepared Pfam full alignments and profile HMMs that are created with the HMMER software as follows:
In order to run RIO locally, the following packages and databases need to be present: HMMER, the Pfam database [ 8 ] , the SWISS-PROT and TrEMBL databases [ 36 ] .