Section: New Software and Platforms


Keywords: Bioinformatics - Genomic sequence - Computational biology - Sequence alignment

Scientific Description

As most of the heuristic DNA local alignment softwares (BLAST, FASTA, PATTERNHUNTER, BLASTZ, LAST...) 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 (most of the design of these seeds is provided by the Iedera tool) to search for more fuzzy repeats, such as non-coding DNA/RNA.

Main features of YASS are: (i) multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off (ii) transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [AG] or pyrimidine to pyrimidine [CT]) (iii) using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies (iv) parameterizable output filter for low complexity repeats (v) reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion), and (vi) post-processing step to group gapped alignments.

Functional Description

YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format : it produces local pairwise alignments.

  • Participants: Laurent Noé and Grégory Kucherov

  • Partners: CNRS - Université de Nancy - Université de Lille

  • Contact: Laurent Noé

  • URL: http://bioinfo.lifl.fr/yass