Improved hit criteria for DNA local alignment.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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 http://www.loria.fr/projects/YASS/.
Noé
Laurent
L
LORIA/INRIA-Lorraine, Villers-lès-Nancy France. Laurent.Noe@loria.fr
Kucherov
Gregory
G
D000465:Algorithms; D000818:Animals; D041321:Chromosomes, Human, X / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D006801:Humans; D008390:Markov Chains; D015233:Models, Statistical; D009345:Neisseria meningitidis / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards*
D004269:DNA, Bacterial; D004271:DNA, Fungal; D004247:DNA