PARSEC: PAtteRn SEarch and Contextualization.
CONCLUSIONS
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.


BACKGROUND
Web site implemented in Java, JavaScript and C++, with all major browsers supported. Freely available at lbgi.fr/parsec. Source code is freely available at sourceforge.net/projects/genomicparsec.
Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) CNRS/INSERM/UDS, 67404, Illkirch, France.
Alexis
A
Allot
Yannick-Noël
YN
Anno
Laetitia
L
Poidevin
Raymond
R
Ripp
Olivier
O
Poch
Odile
O
Lecompte
D000465:Algorithms; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D017711:Nonlinear Dynamics; D011381:Programming Languages; D012984:Software