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

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-suppli...

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Autores principales: Ambrosini, Giovanna, Groux, Romain, Bucher, Philipp
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6041753/
https://www.ncbi.nlm.nih.gov/pubmed/29514181
http://dx.doi.org/10.1093/bioinformatics/bty127
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author Ambrosini, Giovanna
Groux, Romain
Bucher, Philipp
author_facet Ambrosini, Giovanna
Groux, Romain
Bucher, Philipp
author_sort Ambrosini, Giovanna
collection PubMed
description 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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spelling pubmed-60417532018-07-17 PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix Ambrosini, Giovanna Groux, Romain Bucher, Philipp Bioinformatics Applications Notes 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. Oxford University Press 2018-07-15 2018-03-05 /pmc/articles/PMC6041753/ /pubmed/29514181 http://dx.doi.org/10.1093/bioinformatics/bty127 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Ambrosini, Giovanna
Groux, Romain
Bucher, Philipp
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title_full PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title_fullStr PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title_full_unstemmed PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title_short PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
title_sort pwmscan: a fast tool for scanning entire genomes with a position-specific weight matrix
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6041753/
https://www.ncbi.nlm.nih.gov/pubmed/29514181
http://dx.doi.org/10.1093/bioinformatics/bty127
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