HMMER3 · bio.tools
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions.
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GitHub
HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs). HMMER is used by many protein family domain databases and large-scale annotation pipelines, including many …
Bio.SearchIO.HmmerIO package — Biopython 1.75 …
Bio.SearchIO support for HMMER output formats. This module adds support for parsing HMMER outputs. HMMER is a suite of programs implementing the profile hidden Markov models to find similarity across protein sequences. Bio.SearchIO.HmmerIO was tested on the following HMMER versions and flavors: HMMER3 flavors: hmmscan, hmmsearch, …
hmmer
,,hmmer,,,blast。PfamResfamhmmer。 hmmer
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PyHMMER: a Python library binding to HMMER for efficient …
Summary: PyHMMER provides Python integration of the popular profile Hidden Markov Model software HMMER via Cython bindings. This allows the annotation of protein sequences with profile HMMs and building new ones directly with Python. PyHMMER increases flexibility of use, allowing creating queries directly from Python …
API Reference — pyhmmer 0.10.2 documentation
HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is maintained by members of the the …
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HMMER | Ohio Supercomputer Center
HMMER. HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMS). HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability …
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HMMER Manual | i5k
When the HMMER program has finished, your results will be displayed. In 'Download' you can download the input file, the HMMER result (showed in 'Report Details') and the submission details including parameters used in …
NCBI Hidden Markov Models (HMM) Release 12.0 …
Release 12.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available for download. You can search this collection …
hmmer · PyPI
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HMMER Archives
Release 10.0 of the NCBI Hidden Markov models (HMM) used by the Prokaryotic Genome Annotation Pipeline is now available for download.You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.. The 10.0 release contains 15,360 models …
hmmsearch(1) — hmmer — Debian testing — Debian …
DESCRIPTION ¶. hmmsearch is used to search one or more profiles against a sequence database. For each profile in hmmfile, use that query profile to search the target database of sequences in seqdb, and output ranked lists of the sequences with the most significant matches to the profile. To build profiles from multiple alignments, see hmmbuild.
HMMER web server: 2018 update
Affiliations 1 EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; 2 Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
HMMER web server: 2018 update
The HMMER website now provides a single point of entry for those wishing to access the profile HMM libraries supported by EMBL-EBI. The profile HMM libraries have been updated as newer versions became available (Pfam to version 31.0 and CATH-Gene3D to 16.0.0). We have updated the different post-processing procedures that …
HMMER | PSC
HMMER web site; Usage on Bridges-2. To see what versions of HMMER are available and if there is more than one, which is the default, along with some help, type. module spider hmmer. To use HMMER, include a command like this in your batch script or interactive session to load the HMMER module: (note 'module load' is case-sensitive): module ...
PyHMMER — pyhmmer 0.10.3 documentation
HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is maintained by members of the the Eddy/Rivas Laboratory at Harvard University. pyhmmer is a Python module, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the …
HMMER
HMMER is a suite of several programs for biological sequence alignment and database homology search. It uses probabilistic models called "profile hidden Markov models" (profile HMMs) to represent the likely evolutionary homologs of a single sequence or a multiple alignment of a sequence family. A main avenue of research is to improve the ...
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pyhmmer · PyPI
pyhmmer is a Python package, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the HMMER internals, which has the following advantages over CLI wrappers (like hmmer-py ): single dependency: If your software or your analysis pipeline is distributed as a Python package, you can add …
PyHMMER: a Python library binding to HMMER for efficient …
2 Implementation. The original HMMER codebase is organized into several components: a general purpose library for biological sequence manipulation named easel, a core library specific to HMMER named libhmmer, and dedicated CLI tools for building HMMs and performing sequence searches (hmmbuild, hmmsearch, phmmer, etc.).. The Cython …
help | HMMER
There are two flavours of HMMER documentation available: the first concerns the command line use of the tool; the second describes the use of HMMER through this website, which can be accessed using either the web interface or the application program interface (API).. The comprehensive command line documentation provides background on profile HMMs …
HMMER web server: interactive sequence similarity searching
HMMER. BLAST. Comments.; Program phmmer : blastp : Produces similar results in terms of homolog detection. Searching with the sequence from PDB ID 2abl, chain A against PDB yields 244 matches compared with 214 matches for phmmer and blastp, respectively, using an E-value threshold of 0.01 and default search parameters.The …
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NCBI hidden Markov models (HMM) release 4.0 now …
Release 4.0 of the NCBI hidden Markov models (HMM) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. This release contains 17,443 models, …
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