HMMER hmmscan 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 Amino acid sequence homology search chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

HMMER hmmscan specifications

Information


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

Maintainer


  • person_outline Paul Gardner <>

Additional information


http://www.ebi.ac.uk/Tools/pfa/hmmer_hmmscan/help/index.html#sequence

HMMER hmmscan in pipeline

2016
PMCID: 5006616
PMID: 27577548
DOI: 10.1186/s12864-016-3043-1

[…] structurally intact elements were aligned to the forty-five gydb reference sequences using muscle with default settings, and analysed for putative coding regions with gydb protein phmms, using hmmer hmmscan with an e-value threshold of 10−10. domain alignments were inspected and each element was manually classified to either a retroviral genus or the ty1/copia or ty3/gypsy families of ltr […]


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

HMMER hmmscan in publications

 (6)
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] 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 (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) […]

PMCID: 5758725
PMID: 29359195
DOI: 10.1128/mSystems.00123-17

[…] 902 samples sequenced in this study. download table s2, xls file, 0.1 mb., quality metrics and statistics of the concoct genome bins. download table s3, xls file, 0.4 mb., annotations resulting from hmmer hmmscan search against the resfams database using gathering threshold as cutoff values. download table s4, xls file, 19 mb., the infants represented in the column corresponding […]

PMCID: 5006616
PMID: 27577548
DOI: 10.1186/s12864-016-3043-1

[…] structurally intact elements were aligned to the forty-five gydb reference sequences using muscle with default settings, and analysed for putative coding regions with gydb protein phmms, using hmmer hmmscan with an e-value threshold of 10−10. domain alignments were inspected and each element was manually classified to either a retroviral genus or the ty1/copia or ty3/gypsy families of ltr […]

PMCID: 4890743
PMID: 27253872
DOI: 10.1371/journal.pone.0154122

[…] [, ] using an in-house script and to other nrpss and pkss from ncbi_nr (blastp, 1e-5). additional motifs in proteins with amp domains and ketoacyl synthase (ks) domains were identified using hmmer hmmscan (with default settings unless otherwise specified). a degenerate amp domain in the predicted cmtg12bl2 protein cm_1661, homologous with ch_nps6 was identified through manual inspection […]

PMCID: 4673724
PMID: 26664700
DOI: 10.1186/s40793-015-0105-y

[…] of orthologous groups (cogs) was made using blast [] against the latest version of cog database [] with maximal e-value of 10−5. identification of conserved domains families was performed using hmmer hmmscan service []. proteins harboring signal peptides and transmembrane helices were identified with phobius server [] twin-arginine signal peptides were predicted using tatp server [], […]


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

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.

HMMER hmmscan reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review HMMER hmmscan