Analysis & Visualization
The Cofactor Genomics research process
Before making it to our stellar visualization tool, Gentuition™, your data winds its way through our advanced analytics, including contamination screening, alignment/assembly, annotation, functional analysis and mutation detection. Our analyses ensure your project can compete with genome centers no matter how small your lab or project.
Specifically, Cofactor’s back-end software can analyze your sequencing results to determine expression levels, alternative splicing events, nucleotide and insertion/deletion variants, rearrangements, contamination and complex sample species/strain composition. Contigs can be annotated with known and predicted genes, transcription factor binding sites, comparative homologies, protein coding domains, and pathway characterizations. Variants can be categorized as synonymous or non-synonymous, tolerant or intolerant, and coding or non-coding. MicroRNAs, tRNAs, repeats and origins of replication are annotated as well.
But don’t expect a chaos of squiggles and fluorescent blobs; Gentuition™ displays and summarizes all of these results as high-design gene cards. High-design isn’t about pretty, design-naive interfaces, as they often reduce to shambles when faced with the scale of next-gen data. Some even lie there is too much data, or pretend to display it by actually throwing information away. With GentuitionTM, you can see as much or as little of your data as you want, getting an intelligent and revealing graphical display at any level of detail. Zoom in to a single card for a wholly redesigned but familiar-feeling Consed-like view; you can even zoom to the novel nucleotide level view, the Spaghetti PlotTM.
Our novel design lets you “compress” the visual space occupied by vast introns or “fold-out” introns, repeats or other tags altogether. Coverage and other plots scale their detail to any resolution, but important features like your newly discovered SNPs or variants are rendered at every resolution so they are never hidden.
There is no need to “customize” GentuitionTM with 1,000’s of checkboxes or choices from endless menus. You can manipulate our gene cards with a small set of tools that use intelligence and context-sensitivity to finish your work quickly and simply. Related cards can be grouped by hand or automatically into stacks. Stacks automatically tally important aggregate statistics about their cards and can display them alone or contrast them to other stacks. A RolodexTM-like view and stacks that splay open when you push cards towards them means you can quickly scan or find items even in deep stacks. Drag-and-drop to combine stacks, or have two stacks automatically pull out their union.
GentuitionTM goes beyond just viewing. It prioritizes a quickly intelligible list of causative, differentiating, or novel structures and functions and presents findings in plenty of context. It suggests validation assays, quantifies known unknowns and provides publication-ready figures, freeing you to focus on your discovery.
Gentuition is currently undergoing development to handle larger genomes/transcriptomes and we expect this version to be ready the beginning of 2010.
