YASS: enhancing the sensitivity of DNA similarity search.
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.
LORIA/INRIA-Lorraine 615 rue du Jardin Botanique, 54602 Villers-les-Nancy, France. Laurent.Noe@loria.fr
Laurent
L
Noé
Gregory
G
Kucherov
D000465:Algorithms; D003196:Computer Graphics; D023281:Genomics / Q000379:methods; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface