Computational Biology and Bioinformatics


VESPA Platform -- combined views with proteomics data

A desirable approach to systems-level biological research is to iterate between computation and experimentation. Explicitly, by using computational, statistical, and visualization-based techniques to interrogate large datasets, new experimental hypotheses or computational models can be developed and subsequently tested in the laboratory. However, the volume and heterogeneity of data being generated by high-throughput methods has created a need to develop methods to integrate and interpret data both simply and rapidly while providing powerful underlying capabilities for "super-users". We are developing a software platform, Visual Evaluation and Statistics to Promote Annotation (VESPA), targeted at the integration of peptide-centric proteomics data with other forms of high-throughput, qualitative and quantitative data, such as data from Ref-SEQ analyses. At the core, VESPA integrates bottom-up proteomics data with genome level information, i.e., mapping peptides to their respective genome locations. This capability is a necessity in proteogenomics where scientists are correcting either mis-annotations or identifying new genes. The visualization allows the user to observe the location and sequence of peptides that do not match current annotations, as well as offering valuable filtering criteria such as the removal of ambiguous peptides. In addition, the integration capabilities of VESPA support user driven information layering or filtering to be used in the visualization, for example adding peptide confidence scores, cleavage state (fully or partially tryptic), or the number of identifications.

VESPA 1.1.1 includes a number of bug fixes and the addition of loading Ref-SEQ data through .wig and .sam files to be displayed on the the 6-frame translation view and the genome view. Some additional properties of proteins found in the .gff file are displayed. The STEPP score can be calculated and used to search and/or display peptides.


VESPA 1.1.1 is freely available. You can download the appropriate installer below:

Windows (XP, 7)
User Guide

NOTE: The JRE 1.6 (Java Runtime Environment) is required. Please make sure that your machine is already installed with a version of JRE 1.6.



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