HMMER protocols

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HMMER computational protocol

HMMER specifications

Information


Unique identifier OMICS_00996
Name HMMER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 3.1b2
Stability Stable
Source code URL http://hmmer.org/
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/HMMER

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Documentation


Maintainer


  • person_outline HMMER Team <>

Additional information


https://www.ebi.ac.uk/Tools/hmmer/help

Information


Unique identifier OMICS_00996
Name HMMER
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Computer skills Basic
Version 3.1
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/HMMER

Documentation


Maintainer


  • person_outline HMMER Team <>

Additional information


https://www.ebi.ac.uk/Tools/hmmer/help

Publications for HMMER

HMMER IN pipelines

 (205)
2018
PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] which identifies coding regions and detects the longest orf for every transcript in combination with homology results from the swiss-prot database (e-value cut-off: 1e-5) and hmmer (v3.1b2) [54], which searches the peptides for protein domains against the pfam database (release 30.0) [55], a collection of protein family alignments. these sets of amino acid sequences […]

2018
PMCID: 5769438
PMID: 29335005
DOI: 10.1186/s40168-017-0387-y

[…] 80% identity and 80% coverage. each protein family was aligned by muscle v. 3.7 [31] with default parameters and a hidden markov model (hmm) was built for each family with hmmbuild function of the hmmer3 [32] using default parameters. hmmer search function (hmmsearch) was used against uniprotdb for each hmm profile to search homologous proteins for each family of proteins that confer […]

2018
PMCID: 5769438
PMID: 29335005
DOI: 10.1186/s40168-017-0387-y

[…] protein family was aligned by muscle v. 3.7 [31] with default parameters and a hidden markov model (hmm) was built for each family with hmmbuild function of the hmmer3 [32] using default parameters. hmmer search function (hmmsearch) was used against uniprotdb for each hmm profile to search homologous proteins for each family of proteins that confer antibiotic resistance. manual curation […]

2018
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] temperatures ranged from 5 to 32 k, using liquid helium as coolant. the spectrometer was controlled by the xepr software package (bruker)., rnr protein sequences were collected and scored using hmmer (eddy, 2011) hmm profiles in the rnrdb (http://rnrdb.pfitmap.org). atp-cones were identified with hmmer and the pfam atp-cone hmm profile: pf03477 (finn et al., 2010). sequences representing […]

2018
PMCID: 5816582
PMID: 29473008
DOI: 10.7717/peerj.4394

[…] (version 3.0.1). we matched microarray probe sequences to known sequences using blast against the swissprot annotated database (apweiler et al., 2004), identified protein sequence homology using hmmer and pfam (finn, clements & eddy, 2011; finn et al., 2015), and searched for known annotations within eggnog and go databases (the gene ontology consortium, 2015; huerta-cepas et al., 2016). […]

HMMER institution(s)
European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK

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