Improved hit criteria for DNA local alignmentReport as inadecuate

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BMC Bioinformatics

, 5:149

First Online: 14 October 2004Received: 26 July 2004Accepted: 14 October 2004


BackgroundThe hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the selectivity and sensitivity of the whole method.

ResultsIn this paper, we propose two ways to improve the hit criterion. First, we define the group criterion combining the advantages of the single-seed and double-seed approaches used in existing algorithms. Second, we introduce transition-constrained seeds that extend spaced seeds by the possibility of distinguishing transition and transversion mismatches. We provide analytical data as well as experimental results, obtained with the YASS software, supporting both improvements.

ConclusionsProposed algorithmic ideas allow to obtain a significant gain in sensitivity of similarity search without increase in execution time. The method has been implemented in YASS software available at

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-149 contains supplementary material, which is available to authorized users.

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Author: Laurent Noé - Gregory Kucherov


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