YASS (Yet Another Similarity Searcher) is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ …), YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step
- Windows/ Linux / Mac OsX
:: MORE INFORMATION
L. Noe, G. Kucherov,
YASS: enhancing the sensitivity of DNA similarity search, 2005,
Nucleic Acids Research, 33(2):W540-W543.