Section: New Software and Platforms


Keywords: Bioinformatics - Indexation - Sequence alignment - Biological sequences - Approximate string matching

Scientific Description

Approximate string matching of short sequences in a text often starts by a filtering step. That step relies on seed searching, which are shorter than the pattern. Usually in those seeds the number of errors is constrained, to allow more efficient computations. We designed the 01*0 seeds which offer a good trade-off between the number of false positives and filtering time.

Functional Description

We applied the 01*0 seeds to the similarity search of miRNA targets in a reference genome (Bwolo software) and to the similarity search between a pre-miRNA and mature miRNAs (Piccolo software).

  • Participants: Sébastien Bini, Mikaël Salson, Hélène Touzet and Christophe Vroland

  • Partners: CNRS - Université Lille 1

  • Contact: Helene Touzet

  • URL: http://bioinfo.lifl.fr/olo/