Broad Area Colloquium for Artificial Intelligence,
Geometry, Graphics, Robotics and Vision
Assembly and Exploration of the Public Human Genome Working Draft
David Haussler
Howard Hughes Medical Institute
Monday, November 5th, 2001, 4:15PM
Gates B01 http://robotics.stanford.edu/ba-colloquium/
Abstract
A program written by UCSC student Jim Kent, called GigAssembler, is
used to periodically assemble a widely used public draft version of
the human genome sequence using updated data from GenBank at the
National Center For Biotechnology Information (NCBI). This assembly
is steadily improving as the the public sequencing consortium churns
out new data. We will look at the coverage statistics on the latest
assembly, and then look at web tools to explore it, and what they
find. The three most widely used public annotation browsers are the
UCSC Genome browser (genome.ucsc.edu), the Ensembl genome browser
(www.ensembl.org), and the NCBI map viewer
(www.ncbi.nlm.nih.gov/genome/guide), the latter based on NCBI's own
sequence assembly. We will focus on the UCSC browser, which shows a
rich variety of data mapped to the genome sequence, including
predicted genes, expressed sequence tags, full length mRNAs, genetic
and radiation hybrid map markers, cytogenetically mapped clones,
single nucleotide polymorphisms, homologies with mouse and pufferfish,
and more. This data is presented on different tracks of annotation
that are contributed by the annotation team at UCSC and more than a
dozen researchers worldwide. We discuss how web-based data browsers
such as this are accelerating biomolecular and biomedical research,
and how scientists and engineers in other disciplines can contribute
to the study of the human genome.
About the Speaker
David Haussler is an investigator for the Howard Hughes Medical
Institute, he holds the UC Presidential Chair in Computer Science at
the Santa Cruz Campus, he is a consulting professor for the Stanford
Medical School and the University of California San Francisco
Biopharmaceutical Sciences Department, a fellow of the American
Association for Artificial Intelligence (AAAI), and a member of the
nominating committee for the International Society for Computational
Biology. He is currently Director of the Center for Biomolecular
Science & Engineering at UCSC and scientific co-director of the
multi-campus Institute for Bioengineering, Biotechnolgy and
Quantitative Biomedical Research at USCF, UCB and UCSC.
