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HMMER specifications

Information


Unique identifier OMICS_00996
Name HMMER
Alternative name Hmmsearch
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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Versioning


No version available

Documentation


Maintainer


  • person_outline HMMER Team <>

Additional information


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

Information


Unique identifier OMICS_00996
Name HMMER
Alternative name Hmmsearch
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 citations

 (2940)
library_books

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536

[…] alignment produced by the phylogenetic analysis, because isip1 does not belong to a particular protein family in any phmm database, such as pfam. we used the phmm along with the software package hmmer () to retrieve all sequences from the tara oceans metagenome and metatranscriptome that matched our model of isip1. only sequences taxonomically assigned as diatoms and not previously […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] domain of a protein. we used the amino acid sequence of the gene that the snp is located in as input to do “prim-seq-an w/pfam” analysis in annotator [] using default settings which include hmmer against many protein domain databases e.g. smart, pfam to retrieve functional domain information of the protein. later, we annotated whether a snp is located in any functional domain […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] ortholog families with approximately-maximum-likelihood model and bootstrap 100 []., gene family annotation for c. pseudoreteaudii and the other organisms was based on a pfam local database with hmmer version 3.1b1 [, ]. the comparison of gene families across organisms was conducted by cafe with lambda 0.314, p value 0.01 and 1000 random samples []., putative cazymes were identified using […]

library_books

Genome wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.

2018
PMCID: 5944045
PMID: 29743013
DOI: 10.1186/s12864-018-4722-x

[…] model (hmm) profile (pf03514.13) []. the hmm profile was then used to perform hmm searches against annotated protein databases from different genomes with an e-value cutoff of 1e− 5 in the program hmmer 3.1b2 []. to confirm that the predicted proteins contained gras domains, we evaluated them using the smart software [] (http://smart.embl-heidelberg.de/). proteins without gras domain […]

library_books

Transcriptomic analysis of crustacean molting gland (Y organ) regulation via the mTOR signaling pathway

2018
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] and 10,778 (16.3%) predicted peptides/orfs with significant hits, respectively (table ). in addition to the blast analyses, the orf sequences were analyzed to identify predicted pfam domains (hmmer/pfam), transmembrane helices (tmhmm) and signal peptide cleavage sites (signalp). all the outputs from blastx, blastp, hmmer/pfam, tmhmm, and signalp were combined into a single annotation file […]

library_books

Valine glutamine (VQ) motif coding genes are ancient and non plant specific with comprehensive expression regulation by various biotic and abiotic stresses

2018
PMCID: 5941492
PMID: 29743038
DOI: 10.1186/s12864-018-4733-7

[…] motif sequences were downloaded from the pfam database, which were aligned using clustal x2 (http://www.clustal.org/clustal2/). the aligned vq motifs were used to construct the hmm profile using the hmmer v3.1b2 (windows version, http://www.hmmer.org/). the hmm searches were carried out using the order “hmmsearch” under the e-value cutoff at 0.01 against all protein databases. the identification […]


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

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