# YASS : Enhancing the sensitivity of DNA similarity search

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.
Keywords :
Document type :
Conference papers
Domain :

https://hal.inria.fr/inria-00100004
Contributor : Publications Loria <>
Submitted on : Tuesday, September 26, 2006 - 10:13:17 AM
Last modification on : Friday, February 26, 2021 - 3:28:02 PM

### Identifiers

• HAL Id : inria-00100004, version 1

### Citation

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