Our first guest post in our new semi-regular Guest Post series is from Inna Dubchak , principal investigator at the LBNL/JGI group, developers of the VISTA comparative genomics resource (who sponsors a tutorial, free to the users). If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.
I would like to give you a heads up on some new VISTA updates and ongoing development!
Updates: As you probably know from this blog, a new, still free VISTA tutorial is available now. We have introduced a lot of updates to these tools - built new programs, improved the existing ones, and entirely changed the design of the site to make it more up-to-date and convenient.
Main addition to the site – VISTA Point – combines capabilities of the three tools currently available at the site – VISTA Gateway, VISTA Browser, and Text Browser usually used step-by-step. VISTA Point makes analyzing multiple and pairwise genome alignments and extracting relevant numerical data much more straightforward, it is easy to update, expand and add new programs.
Soon: We are actively working on visualizing synteny at scales ranging from whole-genome alignment to the conservation of individual genes, with seamless navigation across different levels of resolution. In our upcoming VISTA-Dot tool we used the concept of two-dimensional “dot-plots”, historically employed in the analysis of local alignment, and an interactive Google-map-like interface to visualize whole-genome alignments. You will be able to get a display and analyze large-scale duplication in plants in one click! It can also be useful in genome assembly and finishing. Another addition coming in the near future, VISTA Synteny Viewer, presents a novel interface as three cross-navigable panels representing different scales of the alignment.
Attention: do not forget to use our whole-genome capabilities – Whole-genome VISTA to align sequence of any quality, from draft to finished, up to 10MB long, and Whole Genome rVISTA to evaluate which transcription factor binding sites (TFBS) are over-represented in upstream regions in a group of genes.