Sentence examples for using the hmmer software from inspiring English sources

The search was accomplished by Hidden Markov model (HMM) analysis using the HMMER software package [ 55].

The UniProt database was searched using the HMMER software and a Hidden Markov Model built from any pepsin homologues found.

Searches using profile Hidden Markov Models (HMMs) from the PFAM database [ 43] were done using the HMMer software package.

A profile HMM was constructed from the alignment of known OR sequences from human, frog, and fish using the HMMER software package (http://hmmer.janelia.org).org

The consensus sequences from combined assembly of both subspecies were also searched against the Pfam-A database using the HMMER software Version 3.0 [ 54].

Profiles unique to the CBS domain were used to screen all predicted proteins using the HMMER software (version 2.3.2;. These unique profiles are for Pfam HMM of CBS domain (accession no. PF00571) [ 83].

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

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].

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