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. 2018 Jul 15;34(14):2483-2484.
doi: 10.1093/bioinformatics/bty127.

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Giovanna Ambrosini  1   2 , Romain Groux  1   2 , Philipp Bucher  1   2
Affiliations

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Giovanna Ambrosini et al. Bioinformatics. .

Abstract

Summary: Transcription factors regulate gene expression by binding to specific short DNA sequences of 5-20 bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or transcription factor binding site model from a public database.

Availability and implementation: The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Screen shot of the PWMScan graphical user interface
See this image and copyright information in PMC

References

    1. Ambrosini G. et al. (2016) The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. BMC Genomics, 17, 938.. - PMC - PubMed
    1. Bailey T.L. et al. (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res., 37, W202–W208. - PMC - PubMed
    1. Khan A. et al. (2017) JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res., 46, D260–D266. - PMC - PubMed
    1. Kulakovskiy I.V. et al. (2017) HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res., 46, D252–D259. - PMC - PubMed
    1. Langmead B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.. - PMC - PubMed

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