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

HMMER articles

HMMER citations

 (71)
2018
PMCID: 5940178

[…] in the detection of deleterious mutations, as we have observed with pfam hmms [21]. each protein sequence was searched against the hmm database using hmmsearch from the hmmer3.0 package (http://hmmer.org). the top scoring model corresponding to each protein was used for analysis (n = 8,060 groups). orthologous groups (ogs) with no corresponding eggnog hmm, or more than one top model hit […]

2018
PMCID: 5870968

[…] genes. to confirm that core genes were not misclassified as accessory genes using blast-based similarity searches, we also classified orthologs based on pfam domain content and order, using hmmer version 3.1 (http://hmmer.org) to characterize domain profiles for all accessory proteins., to identify genes that were differentially conserved across populations, we used a gene enrichment […]

2018
PMCID: 5769542

[…] a set of 100 previously identified hmms for predominantly single-copy bacterial and archaeal markers37,38 were searched against the putative cds of the secondary contigs from each province using hmmer (parameters: hmmsearch --cut_tc). from each province, the set of cds identified by the marker hmms could be used to approximate the total bacterial and archaeal community. markers belonging […]

2018
PMCID: 5753479

[…] 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: 5794259

[…] 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 […]

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

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