HAL will be down for maintenance from Friday, June 10 at 4pm through Monday, June 13 at 9am. More information
Skip to Main content Skip to Navigation
Conference papers

YASS : Enhancing the sensitivity of DNA similarity search

Laurent Noé 1 Gregory Kucherov 1
1 ADAGE - Applying discrete algorithms to genomics
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : We present YASS -- a new tool for computing local similarities in DNA sequences. Similar to many existent algorithms (e.g. BLAST), YASS first searches for small patterns (``seeds'') shared by input sequences and then extends some of those (``hits'') into larger alignments. New features of YASS include, on the one hand, a new transition-constrained seed model and, on the other hand, a flexible group criterion of forming hits out of individual seeds. Computer experiments confirm that the program achieves a good sensitivity/selectivity trade-off compared to existing programs, which makes of YASS an efficient tool for comparing long DNA sequences, such as eukaryotic chromosomes.
Document type :
Conference papers
Complete list of metadata

Contributor : Publications Loria Connect in order to contact the contributor
Submitted on : Tuesday, September 26, 2006 - 10:13:17 AM
Last modification on : Friday, February 4, 2022 - 3:33:22 AM


  • HAL Id : inria-00100004, version 1



Laurent Noé, Gregory Kucherov. YASS : Enhancing the sensitivity of DNA similarity search. Proceedings of the 4th International conference on Bioinformatics of Genome Regulation and Structure - BGRS'2004, Institute of Cytology and Genetics, 2004, Novosibirsk, Russia, pp.289-292. ⟨inria-00100004⟩



Record views