YASS

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.


References in zbMATH (referenced in 5 articles , 1 standard article )

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  2. Egidi, Lavinia; Manzini, Giovanni: Better spaced seeds using quadratic residues (2013)
  3. Chung, Won-Hyoung; Park, Seong-Bae: Hit integration for identifying optimal spaced seeds (2010) ioport
  4. Noé, Laurent; Gîrdea, Marta; Kucherov, Gregory: Designing efficient spaced seeds for SOLiD read mapping (2010)
  5. Noé, Laurent; Kucherov, Gregory: YASS: Enhancing the sensitivity of DNA similarity search. (2005) ioport