Visualization and Exploration of Large Multiple Sequence Alignments

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Speaker
Andrew Walsh
Postdoctoral Fellow, Language Technologies Institute, Carnegie Mellon University

When
-

Where
Newell-Simon Hall 1305 (Michael Mauldin Auditorium)

Description

As the number of available biological sequences grows, new tools will be needed to visualize and explore the large quantities of data in a meaningful way. This is particularly evident in the field of virology, where tens of thousands of sequences are already available for certain viruses. This means that in some cases there are hundreds of unique sequences for single proteins in specific viruses, so that alignment of these sequences is meaningful and potentially fruitful. Here I will present a tool specifically designed for the challenges of visualizing and exploring an alignment containing any number of protein sequences.

Many of the features of this tool will be demonstrated; these include multiple simultaneous linked views, displays which emphasize distributions over lists of data, and views highlighting physicochemical properties. I will also show some applications of the tool to studies of gp160 from HIV-1; these include studies focused on the unique properties of certain strains and on the universal properties of all strains.

Speaker's Bio

Dr. Andrew Walsh is currently a Postdoctoral Fellow in the Language Technologies Institute at Carnegie Mellon University. He is interested in many facets of virus biology, from molecular evolution to the dynamics of transmission and their public health ramifications. He received his PhD from The Johns Hopkins University School of Public Health after doing his undergraduate studies in the Biology department at Carnegie Mellon. He is currently involved in projects on the visualization and statistical analysis of large numbers of virus sequences along with Dr. Roni Rosenfeld and in collaboration with many experimentalists. This work is an effort to integrate his training in biology and statistics and a lifelong fascination with computers.