YASS :: genomic similarity search tool

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What is YASS ?

YASS 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 pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local 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 (as provided for example by iedera).

Main features of YASS are: Yass box

YASS produces the common blast tabular output files ("-d 3" option). Moreover, a small perl script is provided to transform the original extended output ("-d 1" option) into blast output with alignments (which can be directly parsed with Bioperl), axt files, or fasta alignments : yass2blast.pl. Another small php script is provided to transform the original extended output ("-d 1" option) into png dotplot files : yass2dotplot.php.

If you use this program in your work, please cite :

[1]    L. Noe, G. Kucherov YASS: enhancing the sensitivity of DNA similarity search, 2005, Nucleic Acids Research, 33(2):W540-W543.

Of course, your are welcome and always appreciated!

Query YASS Online

You can query YASS from this server: yass.php.

The web interface enables you to run the YASS pairwise alignment tool online, on your DNA sequences, and visualise the pairwise local alignments produced online: Dot-plot view


A non-exhaustive list of papers that use YASS ... I also try to maintain a (try to be) exhaustive list of "spaced seeds" related papers for those interested in this subject. Please let me know if I forget someone ...