CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats

Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Michael, Brown, Kyndall, Kyrpides, Nikos C. and Hugenholtz, Philip (2007) CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8 209-1-209-8. doi:10.1186/1471-2105-8-209

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Author Bland, Charles
Ramsey, Teresa L.
Sabree, Fareedah
Lowe, Michael
Brown, Kyndall
Kyrpides, Nikos C.
Hugenholtz, Philip
Title CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats
Journal name BMC Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2007-06-01
Year available 2007
Sub-type Article (original research)
DOI 10.1186/1471-2105-8-209
Open Access Status DOI
Volume 8
Start page 209-1
End page 209-8
Total pages 9
Place of publication London, England, U.K.
Publisher BioMed Central
Language eng
Abstract Background: 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.
Formatted abstract
Background: 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. Results: 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 proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats. Conclusion: In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over 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.
Keyword DNA repeats
Bacterial genomes
Repetitive Dna
identification
Prokaryotes
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 209, pp. 1-8

Document type: Journal Article
Sub-type: Article (original research)
Collections: ERA 2012 Admin Only
School of Chemistry and Molecular Biosciences
 
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Created: Tue, 29 Nov 2011, 20:34:58 EST by Hong Lee on behalf of School of Chemistry & Molecular Biosciences