YASS: enhancing the sensitivity of DNA similarity search | Zendy

Laurent Noé | Zendy; Grégory Kucherov | Zendy

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YASS: enhancing the sensitivity of DNA similarity search

Author(s) -

Laurent Noé,

Grégory Kucherov

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki478

Subject(s) - upload , biology , smith–waterman algorithm , interface (matter) , computational biology , similarity (geometry) , download , dna , plot (graphics) , sequence alignment , genetics , information retrieval , data mining , bioinformatics , computer science , world wide web , peptide sequence , artificial intelligence , mathematics , image (mathematics) , gene , biochemistry , pulmonary surfactant , gibbs isotherm , statistics

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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