HMMER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HMMER
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Tool usage distribution map

This map represents all the scientific publications referring to HMMER per scientific context
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Associated diseases

This word cloud represents HMMER usage per disease context
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Popular tool citations

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Protocols

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

 (2574)
call_split

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

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] ence 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 associated […]

library_books

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome resolved metagenomics

2018
Biotechnol Biofuels
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] stimates of completeness and potential contamination of 23 bacterial or archaeal genomes constructed from assemblies of MP and AP metagenomes. The first method is based on Hidden Markov Models (using hmmsearch with–cut_tc and–notextw) of 107 ESCGs (Additional file : Table S2) conserved in 95% of all bacteria [], which can also be used to indicate the degree of potential contamination, because thes […]

library_books

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

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

[…] icted as “Deleterious” with the SIFT score equal to or less than 0.05 (Additional file : Table S2). The fourth criterion is to check if the SNPs lie on any functional domain. To do this, we retrieved HMMER results against Pfam and SMART using “Prim-Seq-An w/Pfam” analysis on ANNOTATOR and found that 35 out of the 77 SNPs are located in a functional domain of their proteins. The final criterion was […]

library_books

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

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

[…] 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 the H […]

library_books

Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

2018
BMC Plant Biol
PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3

[…] ates this pathway via a low level of expression at stages S, T and FO.In total, 50 ARFs (Auxin response factors) were identified in our transcriptomic data using getorf [] with minsize set to 150 and hmmsearch [] with all parameters set to default according to descriptions in PlantfDB. After filtering those with low FPKM values, we obtained nine DEGs encoding ARFs (Additional file : Table S9); the […]

library_books

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

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

[…] , HMMER hmmscan (https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk/documentation/man/hmmscan.man) was used to search for sequences against a Pfam-A database (downloaded on April 19, 2016) (http://hmmer.janelia.org/). In addition, transmembrane helical domains, cleavage sites for signal peptides were identified using TMHMM (version number: 2.0c), and SignalP (version number: 4.1) software respe […]


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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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