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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


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 (, the Ensembl genome browser (, and the NCBI map viewer (, 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.


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