PARSEC: PAtteRn SEarch and Contextualization

Bioinformatics. 2013 Oct 15;29(20):2643-4. doi: 10.1093/bioinformatics/btt455. Epub 2013 Aug 7.


Summary: We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a degenerated pattern. The retrieved set of genomic sites can be characterized in terms of (i) conservation in model organisms, (ii) genomic context (proximity to genes) and (iii) function of neighboring genes. These modules allow the user to explore, visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites.

Availability: Web site implemented in Java, JavaScript and C++, with all major browsers supported. Freely available at Source code is freely available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Genome
  • Genomics / methods*
  • Humans
  • Internet
  • Nonlinear Dynamics
  • Programming Languages
  • Software