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Nucleic Acids Research 2005 33(Web Server Issue):W540-W543; doi:10.1093/nar/gki478
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

YASS: enhancing the sensitivity of DNA similarity search

Laurent Noé* and Gregory Kucherov

LORIA/INRIA-Lorraine 615 rue du Jardin Botanique, 54602 Villers-les-Nancy, France

*To whom correspondence should be addressed. Tel: +33 3 83 59 30 11; Fax: +33 3 83 27 83 19; Email: Laurent.Noe{at}loria.fr

Received March 23, 2005. Accepted April 15, 2005.

YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant alignments. A web interface (http://www.loria.fr/projects/YASS/) is available to upload input sequences in fasta format, query the program and visualize the results obtained in several forms (dot-plot, tabular output and others). A standalone version is available for download from the web page.


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