CRISPR Recognition Tool (CRT): a tool for automatic detection ofclustered regularly interspaced palindromic repeats

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Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was compared to CRISPR detection tools, Patscan and ... continued below

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Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah; Lowe,Micheal; Brown, Kyndall; Kyrpides, Nikos C. et al. May 1, 2007.

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Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT also demonstrated superior performance, especially for genomes containing large numbers of repeats. In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, was shown to be a significant improvement over the current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n) in space and O(nm/l) in time.

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  • Journal Name: BMC Bioinformatics; Journal Volume: 8; Journal Issue: 1; Related Information: Journal Publication Date: 06/18/2007

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  • Report No.: LBNL--62881
  • Grant Number: DE-AC02-05CH11231
  • DOI: 10.1186/1471-2105-8-209 | External Link
  • Office of Scientific & Technical Information Report Number: 932791
  • Archival Resource Key: ark:/67531/metadc902858

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Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • May 1, 2007

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  • Sept. 27, 2016, 1:39 a.m.

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Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah; Lowe,Micheal; Brown, Kyndall; Kyrpides, Nikos C. et al. CRISPR Recognition Tool (CRT): a tool for automatic detection ofclustered regularly interspaced palindromic repeats, article, May 1, 2007; United States. (digital.library.unt.edu/ark:/67531/metadc902858/: accessed December 13, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.