Sentence examples for using the hmmer hmmbuild from inspiring English sources

(i) For each reference group, the sequences were aligned [ 27] and their corresponding HMM profile was computed using the HMMER hmmbuild and hmmcalibrate programs [ 30].

All HMMs were constructed using the HMMER package hmmbuild and hmmcalibrate commands, and sequences aligned to the HMMs were extracted from the output of the hmmpfam command (package available at http://hmmer.janelia.org).org

A query may consist of a single sequence, a multiple sequence alignment, or a profile HMM built using the HMMER program hmmbuild.

We used this alignment to make a HMM profile using the HMMER 3.0 utility hmmbuild [ 21, 22] which provides a model of homology for the cydX locus.

The sequence logos of bZIP domains were created using the HMMER online tool (hmmer.janelia.org/search/hmmsearch) [ 30].

The HMMs were trained on this alignment using the HMMer programme's (Eddy, 1998) HMMBuild.

Domains within the sequences were identified by searching against the Pfam database [69] using the HMMER v3 program [70].

Conserved protein domains were identified using the HMMer package [ 83].

HET domain [ 15, 33] proteins were identified using the HMMer package as described in Methods.

From the alignments, sequence Hidden Markov Models (HMMs) were constructed using the HMMER 2.2 package [ 30].

Alternatively, profile-based search methods using the HMMER algorithm may also be used whenever pre-computed sequence profiles are available.