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CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 b...
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933234/ https://www.ncbi.nlm.nih.gov/pubmed/17537822 http://dx.doi.org/10.1093/nar/gkm360 |
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author | Grissa, Ibtissem Vergnaud, Gilles Pourcel, Christine |
author_facet | Grissa, Ibtissem Vergnaud, Gilles Pourcel, Christine |
author_sort | Grissa, Ibtissem |
collection | PubMed |
description | Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php. |
format | Text |
id | pubmed-1933234 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-19332342007-07-31 CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Grissa, Ibtissem Vergnaud, Gilles Pourcel, Christine Nucleic Acids Res Articles Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php. Oxford University Press 2007-07 2007-05-30 /pmc/articles/PMC1933234/ /pubmed/17537822 http://dx.doi.org/10.1093/nar/gkm360 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Grissa, Ibtissem Vergnaud, Gilles Pourcel, Christine CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title | CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title_full | CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title_fullStr | CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title_full_unstemmed | CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title_short | CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
title_sort | crisprfinder: a web tool to identify clustered regularly interspaced short palindromic repeats |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933234/ https://www.ncbi.nlm.nih.gov/pubmed/17537822 http://dx.doi.org/10.1093/nar/gkm360 |
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