Sentence examples for using the hmmer package from inspiring English sources

The analysis of functional domains was carried out using the HMMER package [49].

Putative proteins were also compared to two sets of hidden Markov models (HMMs): Pfam HMMs [95], and TIGRFAMs [96] using the HMMER package [97].

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].

It aims at identifying homologous sequences by constructing/applying pHMMs using the HMMER package.

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

For the comparison to the CEGMA data set [ 35], we used the hmmer package (version 3.0) to detect hits (e-value < 0.001) to any of the CEGMA profile HMMs.

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

Although C2H2 subtype Zn fingers are not annotated by Interpro as transcription factors they are DNA binding and frequently have this role, so have been included in the transcription factor set. Bit scores reported in the text are for comparisons of the EH1hox HMM against the target sequence using the HMMER software package [ 39].

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