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Welcome to VENN!
- PURPOSE: VENN is an integrative computer program for mapping protein sequence conservation among homologues onto a three dimensional structure of a protein. VENN was named after John VENN, the inventor of VENN diagrams, because VENN can be used to explore the interaction of sequence and structure to identify important functional regions in proteins. The only input needed in a VENN analysis is an experimental or model PDB structure identifier (e.g. 1EX4);alternative site for structure models. VENN retrieves and interprets the PDB file to identify different structure chains. Protein sequences with sequence similarity to each chain are automatically retrieved from the EBI and a list of upto 500 such sequences is presented to the user. The user selects sequences using canned strategies or by their own ad hoc selections. VENN then aligns the protein sequences, calculates a heatmap for conservation of each amino acid position and plots the heatmap onto the protein structure. Different strategies for selecting groups of sequences can be used to identify functional regions and specificity determinants in gene families.
Downloads and Tutorials
Citing VENN
- We ask you to cite VENN whenever VENN is used for research that results in a publication or if a figure is made using VENN. This helps us support VENN and create new version with more capabilities. VENN is a product of the laboratories of Martin R. Schiller and Michael R.Gryk written by Jay Vyas. Other useful software from these labs are Minimotif Miner, CONNJUR, and HIV toolbox is coming in the Summer of 2009.
- PMID: 19656955. Vyas, J., Gryk, M.R., & Schiller, M.R. (2009) VENN, a tool for titrating sequence conservation onto protein structures. Nucleic Acids Research
- VENN was funded by NIH grants GM079689, AI078708, and EB001496.
How VENN works
- VENN works by constructing a mysql data mart on the client machine on which it runs. The data mart is incrementally populated by web service and xml derived results for homology and structural data. This 'mini - mart' is private to your computer, and is not accessible to anyone in the outside world. Thus, you can be ensured that the information, analyses, and figures you produce with VENN are secure. That said, VENN occasionally needs to perform outgoing requests (for example to download structural coordinates, or to run BLAST against Uniparc/Uniprot via external web services). If you have problems running VENN, they are most likely related to stringent blocking of web requests by security features which you have enabled on your machine. Try turning off your firewall. Feel free to contact us (jayunit100@gmail.com) if these issues do not lend themselves to any prompt resolution. VENN supports highly customizable workflows by enabling users to apply ad hoc 'filters' to existing selection of homologs. Such filters enable a process which we call 'titration' , that is, a process by which specificity residues can be incrementally determined by increasingly deviant selections of sequences.
