Friday, September 6, 2013

Fwd: PAVIS: a tool for Peak Annotation and Visualization

Fwd: please follow footer link

PAVIS: a tool for Peak Annotation and Visualization: "

Summary: We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon, or 5'/3' -UTR. PAVIS reports the relative enrichment p-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements thus supporting downstream hypothesis generation.

Availability: PAVIS is publicly accessed at http://manticore.niehs.nih.gov/pavis.

Contact:li3@niehs.nih.gov

Supplementary information: Supplementary data are available at Bioinformatics online

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(Via Bioinformatics - Advance Access.)