PARSEC: PAtteRn SEarch and Contextualization | Zendy

Alexis Allot | Zendy; Yannick-Noël Anno | Zendy; Laetitia Poidevin | Zendy; Raymond Ripp | Zendy; Olivier Poch | Zendy; Odile Lecompte | Zendy

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PARSEC: PAtteRn SEarch and Contextualization

Author(s) -

Alexis Allot,

Yannick-Noël Anno,

Laetitia Poidevin,

Raymond Ripp,

Olivier Poch,

Odile Lecompte

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt455

Subject(s) - contextualization , computer science , context (archaeology) , computational biology , java , biology , genome , set (abstract data type) , parsec , gene , genetics , programming language , paleontology , stars , computer vision , interpretation (philosophy)

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.

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