YASS is a similarity search tool of genomic (DNA/RNA) sequences in fasta or plain text format (it produces pairwise local alignments). This tool is currently developed and maintained by L. Noe and G. Kucherov of the Bioinfo/Sequoia group. Like most of heuristic DNA local alignment algorithms (BLAST, FASTA, PATTERNHUNTER, BLASTZ ...) YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic "homology" search tool enables to search more fuzzy repeats, as non-coding DNA/RNA.
