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

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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⟩

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