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.

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Laurent Noé, Gregory Kucherov
• Keywords: BMCBI 2004, Heuristic Local Alignment, Hit Criterion, Key Component