PWMScan protocols

View PWMScan computational protocol

PWMScan 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 Transcription factor binding site prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Versioning


Add your version

Maintainer


  • person_outline giovanna.ambrosini <>

Additional information


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

Publication for PWMScan

PWMScan in pipeline

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

[…] with a p-value cutoff of 0.01., 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, […]


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

PWMScan in publications

 (15)
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 […]

PMCID: 5338035
PMID: 28256515
DOI: 10.1038/ncomms14656

[…] were lost by the addition of sb525334 (). thus, ep3-mediated reparative ly6clow mo/mp recruitment and neovascularization in infarcted hearts is dependent on tgfβ1 signalling., through the pwmscan tool, 4 and 2 potential smad binding elements (sbes) were predicted in the promoter of murine cx3cr1 (s1–4) and vegf (s1′–2′) genes, respectively (). however, the fragments containing s3 […]

PMCID: 5570574
PMID: 28737489
DOI: 10.7554/eLife.26733.032

[…] identification by comparing chip sample over input sample with default parameters ()., the 5’- and 3’- flanking regions (−5000 to +5000 bp) of sox2 were scanned for nfat binding sequences using pwmscan (). the significance of the predicted sites was evaluated statistically using a permutation-based method and comparison with occurrence of the motif in background genomic sequences […]

PMCID: 5348575
PMID: 27593933
DOI: 10.1038/onc.2016.307

[…] to the manufacturer's instructions. the transwell filters were visualized with a microscope (te300, nikon) and the number of cells was counted. this assay was repeated at least three times., pwmscan was used for the computational prediction of the foxm1 downstream targets., the known foxm1-binding sites are represented in terms of the pwm, as annotated in the transfac database, […]

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

[…] with a p-value cutoff of 0.01., 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, […]


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

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).

PWMScan reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PWMScan