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Open Access Methodology article

Improved hit criteria for DNA local alignment

Laurent Noé* and Gregory Kucherov

Author Affiliations

LORIA/INRIA-Lorraine, 615, rue du Jardin Botanique, B.P. 101, 54602 Villers-lès-Nancy France

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BMC Bioinformatics 2004, 5:149  doi:10.1186/1471-2105-5-149

Published: 14 October 2004



The 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.


In 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.


Proposed 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 webcite.