PWMScan statistics

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Citations per year

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

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

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Popular tool citations

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PWMScan specifications

Information


Unique identifier OMICS_27367
Name PWMScan
Interface Web user interface
Restrictions to use None
Output data A total number of PWM matches and a sequence logo reflecting the letter-probabilities of the input matrix.
Output format BEDdetail
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Plasmodium falciparum
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus laevis
    • Xenopus tropicalis

Maintainer


  • person_outline giovanna.ambrosini

Additional information


https://sourceforge.net/projects/pwmscan/

Information


Unique identifier OMICS_27367
Name PWMScan
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Output format BEDdetail
Operating system Unix/Linux
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Medium
Version 1.1.7
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Plasmodium falciparum
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus laevis
    • Xenopus tropicalis

Download


download.png

Versioning


No version available

Maintainer


  • person_outline giovanna.ambrosini

Additional information


https://sourceforge.net/projects/pwmscan/

Publication for PWMScan

PWMScan citations

 (10)
library_books

Ritornello: high fidelity control free chromatin immunoprecipitation peak calling

2017
Nucleic Acids Res
PMCID: 5716106
PMID: 28981893
DOI: 10.1093/nar/gkx799

[…] The annotated motifs specific to the TFs are downloaded from the JASPAR CORE 2014 motif library (). Genomic locations that match the position weight matrix of each JASPAR motif were identified using PWMScan with default P-value cutoff at 0.00001 (). Predicted peaks whose binding centers are within 100 bp from the corresponding JASPAR motif are classified motif containing. The peaks found by Ritor […]

library_books

TCF21 and the environmental sensor aryl hydrocarbon receptor cooperate to activate a pro inflammatory gene expression program in coronary artery smooth muscle cells

2017
PLoS Genet
PMCID: 5439967
PMID: 28481916
DOI: 10.1371/journal.pgen.1006750

[…] ) were obtained from the JASPAR database (http://jaspar.genereg.net) []. TCF12 PWM was used as it has the same binding motif as TCF21. Human genome hg19 was scanned with the two JASPAR matrices using PWMScan—Genome-wide PWM scanner (http://ccg.vital-it.ch/pwmtools/pwmscan.php). Position weight matrix sites were counted in windows of various lengths surrounding centered features using the Feature c […]

library_books

Activation of E prostanoid 3 receptor in macrophages facilitates cardiac healing after myocardial infarction

2017
Nat Commun
PMCID: 5338035
PMID: 28256515
DOI: 10.1038/ncomms14656

[…] d ±500 bp of the transcription start sites of the CX3CR1 and VEGF gene from the UCSC genome browser database was analysed for putative Smad binding element (SBE) motifs in TRANSFAC version 10.2 using PWMSCAN. A match score with a P value <5 × 10−6 was considered to indicate a high-confidence binding site prediction. […]

library_books

Genome wide recruitment profiling of transcription factor Crz1 in response to high pH stress

2016
BMC Genomics
PMCID: 4992276
PMID: 27544903
DOI: 10.1186/s12864-016-3006-6

[…] To search for putative CDREs at the ChIP-Seq peaks a matrix scan of the S. cerevisiae genome was performed at the PWMTools website (http://ccg.vital-it.ch/pwmtools/pwmscan.php) of the Swiss Bioinformatics Institute. The position weight matrix (PWM) for Crz1 reported by Badis and coworkers [] was used as a reference with a p-value cutoff of 10−3. In parallel, a p […]

library_books

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci

2016
Nat Commun
PMCID: 4941121
PMID: 27386823
DOI: 10.1038/ncomms12092

[…] ing the columns so that the base composition of the randomized matrix remains the same as the JUN::FOS matrix to eliminate potential base composition bias. Whole-genome matrix scan was performed with PWMScan—genome-wide PWM scanner (http://ccg.vital-it.ch/pwmtools/pwmscan.php). PWM scan threshold was set to 0.001 to get approximately same number of sites as in AP-1 (randomized motif scan against h […]

call_split

Deciphering the genomic targets of alkylating polyamide conjugates using high throughput sequencing

2016
Nucleic Acids Res
PMCID: 4872120
PMID: 27098039
DOI: 10.1093/nar/gkw283
call_split See protocol

[…] ks containing identified binding sites were considered as significant enrichment regions (total of 355 882 peaks). Analysis pipelines agplus (), Position Weight Matrix model generation and evaluation-PWMScan (http://ccg.vital-it.ch/pwmscan) (,), ChIP-Cor Analysis Module (http://ccg.vital-it.ch/chipseq/chip_cor.php) and various platforms of the Signal Search Analysis Server (http://ccg.vital-it.ch/ […]


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PWMScan institution(s)
The Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
PWMScan funding source(s)
Supported by the Swiss Institute of Bioinformatics and Swiss Federal Institute of Technology Lausanne (EPFL).

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