Improved hit criteria for DNA local alignmentReportar como inadecuado




Improved hit criteria for DNA local alignment - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Bioinformatics

, 5:149

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

Abstract

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 http:-www.loria.fr-projects-YASS-.

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

Download fulltext PDF



Autor: Laurent Noé - Gregory Kucherov

Fuente: https://link.springer.com/



DESCARGAR PDF




Documentos relacionados