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

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...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz
• Keywords: BMCBI 2007, Detection Tools, Repetitive Sequences, Tool