page_title: HMMER
hierarchical_section_title: HMMER
caption_attribution_description: English: The boxes in yellow are the match states (M). In the M state the probability distribution is the frequency of the amino acids in that position. The row of diamond shaped states are insert states (I) which are used to model highly variable regions in the alignment. The circular states are delete states (D). These are called silent states since they do not match any residues, and they are there merely to make it possible to jump over one or more columns in the alignment.The final probabilistic model conveys the estimation of the observed frequencies of the amino acids in each position, as well as the transitions between the amino acids derived from the observed occupancy of each position in a multiple sequence alignment.&#91;1&#93;
context_page_description: HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. It detects homology by comparing a profile-HMM to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM. Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the hmmbuild program. The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. HMMER is a console utility ported to every major operating system, including different versions of Linux, Windows, and Mac OS.
  HMMER is the core utility that protein family databases such as Pfam and InterPro are based upon. Some other bioinformatics tools such as UGENE also use HMMER.
  HMMER3 also makes extensive use of vector instructions for increasing computational speed.
context_section_description: HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.  It detects homology by comparing a profile-HMM to either a single sequence or a database of sequences.  Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM.  Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the hmmbuild program.  The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. HMMER is a console utility ported to every major operating system, including different versions of Linux, Windows, and Mac OS.
  HMMER is the core utility that protein family databases such as Pfam and InterPro are based upon. Some other bioinformatics tools such as UGENE also use HMMER.
  HMMER3 also makes extensive use of vector instructions for increasing computational speed.  This work is based upon earlier publication showing a significant acceleration of the Smith-Waterman algorithm for aligning two sequences.
caption: A profile HMM modelling a multiple sequence alignment
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