Sentence examples for using the hmmer hmmsearch from inspiring English sources

We then searched all the HMM profiles against the sequences annotated with a valid four-digit EC number available in Swiss-Prot release 56.7 using the HMMER hmmsearch program [ 30]).

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

All predicted protein sets were initially searched using the HMMER 3.0 package (http://hmmer.org/, last accessed November 29, 2013) function hmmsearch (Eddy 2011) with default settings using the Ins_allergen_rep.hmm for PF06757 (http://pfam.janelia.org/, last accessed November 29, 2013) as the query.

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

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].

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

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].

Translated peptide sets for the six model genomes were combined and subjected to the HMMER hmmsearch option using the above criteria.

Starting with protein sequences annotated with the Pfam domain PF00234 (plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor), we scanned maize proteome sequences using the hmmsearch from the HMMER 3.0 package [ 50] with default parameters.