STELLAR: fast and exact local alignments.
STELLAR: fast and exact local alignments.
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DOI：
10.1186/1471-2105-12-s9-s15
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发表时间：
2011-10-05
影响因子：
3
通讯作者：
Reinert K
中科院分区：
文献类型：
--
作者：
Kehr B;Weese D;Reinert K
基因组序列的大规模比较需要可靠的工具来搜索局部比对。实际的局部比对器通常是快速的，但启发式的，因此有时会错过重要的匹配。我们在这里提出的本地成对比对器STELLAR，它对ε-比对具有完全的灵敏度，即保证报告给定的最小长度和最大错误率的所有本地比对。对准器由滤波和校验两个步骤组成。我们应用SWIFT算法进行无损过滤，并开发了一种新的验证策略，我们证明是准确的。我们的模拟和真实的基因组数据的结果证实和量化的猜想，启发式工具，如BLAST或BLAT错过了很大比例的显着的本地比对。STELLAR在非常长的序列上是非常实用和快速的，这使得它成为在编辑距离模型下找到基因组序列之间的局部比对的合适的新工具。在http://www.seqan.de/projects/stellar上可以免费获得Linux、Windows和MacOSX的二进制文件。源代码随SeqAn C++库版本1.3和更高版本在http://www.seqan.de上免费分发。
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. We present here the local pairwise aligner STELLAR that has full sensitivity for ε-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. 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 http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.