HMMER protocols

View HMMER computational protocol

HMMER statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Domain prediction Amino acid sequence homology search Fold recognition chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Download


Versioning


Add your version

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 in pipelines

 (461)
2018
PMCID: 5722264
PMID: 29236932
DOI: 10.1590/0074-02760170179

[…] i). l. longipalpis putative chitinases annotated from ests deposited in genbank were added to the analysis. regions corresponding to the catalytic domains from these proteins were selected using the hmmer 3.1 program (hmmer.org) and the hmm model glyco_ hydro_18 (pf00704). multiple alignments using the catalytic domain sequences were performed using the clustalw2 program. the phylogenetic tree […]

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) [], which searches the peptides for protein domains against the pfam database (release 30.0) [], a collection of protein family alignments. these sets of amino acid sequences […]

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

[…] of 80% identity and 80% coverage. each protein family was aligned by muscle v. 3.7 [] with default parameters and a hidden markov model (hmm) was built for each family with hmmbuild function of the hmmer3 [] 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 […]

2018
PMCID: 5769542
PMID: 29337314
DOI: 10.1038/sdata.2017.203

[…] a set of 100 previously identified hmms for predominantly single-copy bacterial and archaeal markers, 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: 5778769
PMID: 29357911
DOI: 10.1186/s13071-017-2561-2

[…] was used to identify the proportion of the core eukaryotic genome coverage. we used hmm profiles for 458 core eukaryotic proteins as provided by the core eukaryotic genome dataset (cegma) [] and hmmer searches with the hmmscan command and the -t 40 and --domt 40 filters, as described in []. following the same approach, a benchmarking universal single-copy orthologs (busco) sets for arthropod […]


To access a full list of citations, you will need to upgrade to our premium service.

HMMER in publications

 (2814)
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 […]

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 […]

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 […]

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 […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

HMMER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review HMMER