hhsuite
sensitive protein sequence searching based on HMM-HMM alignment
Command lineScience
Not tested on a device yet. What that means
Commands in the package
a3m_database_extracta3m_database_filtera3m_database_reducea3m_extracta3m_reduceffindex_applyffindex_buildffindex_from_fastaffindex_from_fasta_with_splitffindex_getffindex_modifyffindex_orderffindex_reduceffindex_unpackhhalignhhalign_omphhblitshhblits_ca3mhhblits_omphhconsensushhfilterhhmakehhsearchhhsearch_omp
About hhsuite
From Debian's package description
HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
This package contains HHsearch and HHblits among other programs and utilities.
HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling.
HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.
From Debian's description of the hhsuite package, under that package's license.
Dependencies
Depends on
Related apps
- snaplocation of genes from DNA sequence with hidden markov modelCommand line
- mummerEfficient sequence alignment of full genomesCommand line
- fsaFast Statistical Alignment of protein, RNA or DNA sequencesCommand line
- ncbi-blast+next generation suite of BLAST sequence search toolsCommand line
- gbrowseGMOD Generic Genome BrowserCommand line
- cclibParsers and algorithms for computational chemistryCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the hhsuite package, under that package's license.
- Description: Debian's description of the hhsuite package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.