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Bioinformatics. 2016 Dec 1;32(23):3670-3672. Epub 2016 Aug 13.

Gene Slider: sequence logo interactive data-visualization for education and research.

Author information

1
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada.

Abstract

Gene Slider helps visualize the conservation and entropy of orthologous DNA and protein sequences by presenting them as one long sequence logo that can be zoomed in and out of, from an overview of the entire sequence down to just a few residues at a time. A search function enables users to find motifs such as cis-elements in promoter regions by simply 'drawing' a sequence logo representation of the desired motif as a query. In addition to displaying user-supplied FASTA files, our demonstration version of Gene Slider loads and displays a rich database of 90 000+ conserved non-coding regions across the Brassicaceae indexed to the TAIR10 Col-0 Arabidopsis thaliana sequence. It also displays transcription factor binding sites, enabling easy identification of regions that are both conserved across multiple species and may contain transcription factor binding sites.

AVAILABILITY AND IMPLEMENTATION:

Freely available on the web at: http://www.bar.utoronto.ca/GeneSlider and also as an app on http://araport.org Website implemented in JavaScript and Processing.js with all major browsers supported. Source code available under GNU GPLv2 at SourceForge: https://sourceforge.net/projects/geneslider/ CONTACT: nicholas.provart@utoronto.ca.

PMID:
27522081
DOI:
10.1093/bioinformatics/btw525
[Indexed for MEDLINE]

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