Mathematical Biology Seminar
Mark Yandell
Department of Human Genetics, Eccles Institute of Human Genetics
University of Utah
"Using Annotated Genomes as resources for explorations of gene structure,
function and evolution"
We have developed an open-source software library designed to facilitate
the use of genome annotations as substrates for computation and
experimentation. We call the library 'CGL' an acronym for Comparative
Genomics Library, and pronounce it 'Seagull'. CGL provides an informatics
infrastructure for a lab, department or research institute engaged in the
large-scale analysis of genomes and their annotations. To date we have
employed CGL in two major projects-one largely experimental in nature, and
the other computational.
The goal of the experimental project has been to obtain an accurate
estimate of the true number of protein-coding genes in D. melanogaster.
Estimates of gene number have been one of the most hotly debated aspects of
annotation in every genome sequenced to date. D. melanogaster is no
exception. In order to resolve this issue we've collected over 12,000
additional gene-predictions from a variety of sources and used CGL to
coordinate a large, PCR-based, prediction validation project. Our results
demonstrate the utility of CGL as tool for genome management, and speak to
the completeness and accuracy of a key genome's annotations.
The second project is comparative in its focus. We have used CGL to carry
out a very large-scale study of the evolution of gene-structure using
eleven different animal genomes and their associated annotations; perhaps
the largest comparative genomics analysis to date. CGL makes it possible to
compare annotations to one another in new ways, and thus opens new
perspectives on genes and their evolution. Our results provide a glimpse of
how gene structures have evolved and diversified over the last 500 million
or so years of animal evolution.
|
Mathematical Biology Program
Department of Mathematics
University of Utah
155 South 1400 East Room 233
Salt Lake City, UT 84112
rasmusse@math.utah.edu
|
|
