SCRoftware

Welcome to the VisSPA page. VisSPA is protected by copyright but free of charge. Before you download software you need to read my disclaimer (below).

This software is "Hello-ware". When you register on the download server, all you have to provide is a valid email address, but I would love to hear what organism(s) you are studying, and where you are located. The email address allows me to:

• notify you of updates and bug fixes
• get some satisfaction from knowing that I did not waste this effort

VisSPA is a user-friendly Windows program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were initially inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs). The logos were inspired by the work of Tom Schneider (of NCI) and Jan Gorodkin and colleagues (DTU, Denmark)..

The program (as well as its icon and name) is protected by copyright but is distributed free of charge. Please do not give it to others - just send them here so that I can get some indication of how and where the software is being used. This helps me prioritize projects, prioritize enhancements, and notify users when a new release is available.

Acknowledgments:

I want to acknowledge:

• Bette Korber of the Theoretical Biology group at the Los Alamos National Laboratories, who developed the Viral Epidemiology Signature Pattern Analysis (VESPA) software. As noted in the VisSPA Help file, the analyses displayed on the "Consensus and Compare" and "Detailed Analysis" tabs of VisSPA are based on similar results generated by VESPA, though I did not use or refer to the VESPA source code at all, so any errors in VisSPA are mine. VESPA is available here: http://www.hiv.lanl.gov/content/hiv-db/HTML/vespa.html, and was described in this publication: Korber, B., and G. Myers. 1992. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res. Hum. Retroviruses 8:1549-1560
• Thomas D. Schneider, who first described sequence logos in this publication: T. D. Schneider and R. M. Stephens, Sequence Logos: A New Way to Display Consensus Sequences Nucl. Acids Res. 18: 6097-6100, 1990 and whose fascinating web site is here: http://www-lmmb.ncifcrf.gov/~toms/.
• Jan Gorodkin, who described type 2 logos in this publication: Gorodkin J, Heyer LJ, Brunak S, Stormo GD. Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci. 1997 Dec;13(6):583-6 and has a web server for generating a variety of logos here:
  • RNA: http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html
  • proteins: http://www.cbs.dtu.dk/~gorodkin/appl/plogo.html
• Don Gilbert at Indiana University, who generously put the ReadSeq source code (ca. 1990) in the public domain. Dr. Gilbert who is responsible for how well file formats are detected. However, I am responsible for any bugs in the format detection, as I have changed the code significantly, e.g. adding detection of PHYLIP, Nexus, and other formats.