UPDATE: Gene Slider is now available through the App Store on Araport.org!
Gene Slider is a data visualization tool for exploring the conservation or entropy of nucleotides (A,T,C or G) in homologous genes over multiple organisms. The taller letters are highly conserved and represent the proportion of species that share the same nucleotide at each position in a gene. The smaller letters occur when there is entropy at that position, with different organisms having evolved to use different nucleotides at various positions.
I wrote this tool in Processing with Nicholas Provart and Asher Pasha. We presented it at the BioVis 2013 “Redesign the Sequence Logo” contest, part of the Vis 2013 conference in Atlanta. We also presented it at the Arabidopsis Information Portal Developer Workshop at the Texas Advanced Computing Center, November 2014.
Gene Slider loads DNA and protein FASTA files, up to 10,000 sequences long and 5,000 bases wide, to make Sequence Logos that you can interact with. Users can explore the entropy or conservation of homologous genes from a broad overview all the way down to just a few residues at a time. A search function enables users to quickly find query motifs by simply “drawing” a SeqLogo in the search panel. You can click any base to drill down into the data. You can also save, load and share your work sessions.
Gene Slider enables users to visually identify promoter regions and other interesting motifs, which may help in hypothesis generation.