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BMCBI
2004

Improved hit criteria for DNA local alignment

9 years 6 hour ago
Improved hit criteria for DNA local alignment
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.
Laurent Noé, Gregory Kucherov
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Laurent Noé, Gregory Kucherov
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