HMMER hmmscan statistics

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Number of citations per year for the bioinformatics software tool HMMER hmmscan

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HMMER hmmscan specifications


Unique identifier OMICS_19710
Name HMMER hmmscan
Alternative name hmmscan
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA, UniProtKB/Swiss-Prot
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Paul Gardner

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HMMER hmmscan citations


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

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

[…] ntig sequences. These peptide sequences were annotated via BLASTp against known databases with a cutoff of 1e−5. In order to identify conserved protein families among the predicted peptide sequences, HMMER hmmscan ( was used to search for sequences against a Pfam-A database (downloaded on April 19, 2016) (http://hm […]


Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

Front Microbiol
PMCID: 5936773
PMID: 29760683
DOI: 10.3389/fmicb.2018.00703

[…] using FrameBot () against the nifH protein reference set. (5) Homologous genes to the nifH gene (bchX, chlL, bchL, and parA) were filtered out against the HMM nifH_ChlL_bchX.hmm (see above) using the hmmscan command in HMMER. Only OTU representatives that scored highest against the nifH model compared with the bchX and chlL-bchL models were retained. (6) OTU classification and phylogenetic placeme […]


Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors

BMC Genomics
PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] identify the proportion of the core eukaryotic genome coverage, as described []. We used HMM profiles for 458 core eukaryotic proteins as provided by the CEGMA dataset [] and HMMER3 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 [] was used to assess tr […]


Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] rotein family from Pfam database ( and carbohydrate-binding modules from CAZy ( and dbCAN v5.0 ( databases using hmmpress and hmmscan utilities in HMMER3 ( with profile-specific GA (gathering) thresholds. Furthermore, the predicted secretomes in Aspergillus species were annotated with protein family and dom […]


Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] esent in the bacterial phylogeny shown in . Sequences containing at least 100 amino acids upstream of the FGE domains were selected. Annotated domains within these sequences were identified using the hmmscan function of HMMER3 []. Homologs of the gliding motility protein GldK, whose N-terminal domain is not annotated, were manually added based on similiarity to the known GldK sequence from Flavoba […]


Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] . 2014). SMURF ( was used to predict putative secondary metabolite genes and clusters with the default parameters except that terpene cyclases (TCs) were identified by Hmmscan in HMMer version 3.0 [] using the PFAM domain PF03936 (e-value, 1E-03). Candidate transcription factors (TFs) were identified with Hmmscan based on reported TF domains [] with a cut-off e-valu […]

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HMMER hmmscan institution(s)
The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
HMMER hmmscan funding source(s)
Supported by a Carlsberg Foundation Grant (21-00-0680) and a grant from the Danish FNU.

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