HH-suite3 for fast remote homology detection and deep protein annotation

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 473 - 15
• Main Authors: Steinegger, Martin, Meier, Markus, Mirdita, Milot, Vöhringer, Harald, Haunsberger, Stephan J., Söding, Johannes
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 14.09.2019; BioMed Central; BMC
• Subjects: Algorithm; Algorithms; Alignment; Amino acid sequence; Amino acid sequencing; Annotations; Computer programs; Explosions; Freeware; Genomics; Homology; Homology (Biology); Homology detection; Markov chains; Markov processes; Message passing; Methods; Observations; Open source software; Parallel processing; Profile HMM; Protein alignment; Protein folding; Protein structure; Proteins; Searching; Sequence search; SIMD; Software; Software packages; Source code; Structure-function relationships; Suites (Software); Viterbi algorithm detectors; United States

HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. We developed a single-instructi...