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STELLAR: fast and exact local alignments

By Weese David, Kehr Birte and Reinert Knut


<p>Abstract</p> <p>Background</p> <p>Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches.</p> <p>Results</p> <p>We present here the local pairwise aligner STELLAR that has full sensitivity for <it>ε</it>-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments.</p> <p>Conclusions</p> <p>STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at <url>http://www.seqan.de/projects/stellar</url>. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at <url>http://www.seqan.de</url>.</p

Topics: Biology (General), QH301-705.5, Science, Q, DOAJ:Biology, DOAJ:Biology and Life Sciences, Computer applications to medicine. Medical informatics, R858-859.7
Publisher: BioMed Central
Year: 2011
DOI identifier: 10.1186/1471-2105-12-S9-S15
OAI identifier: oai:doaj.org/article:2781ede6c7b34c9f95d5b38b7c21d855
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