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Genomes to Life Contractor-Grantee Workshop I
Arlington, Virginia, February 9-12, 2003

Workshop Breakout Session

Comparative Genomics: New Approaches & Insights

Session Chairs:

  • Jim Fredrickson (Pacific Northwest National Laboratory)
  • Susan Lucas (The Joint Genome Institute)

DOE Contact: Dan Drell (BER)

Genome sequence analysis is providing new insights into evolution, biodiversity, gene transfer, and is even challenging the current concept of species in prokaryotic biology. Comparative genomics is an evolving discipline that is benefiting from expanding genome sequencing efforts. The objective of this session is to explore several of the new approaches and scientific insights that are evolving from comparative genomics and to discuss how high-throughput gene sequencing can best facilitate advances in comparative genomics. The format for this breakout session includes a series of overviews by George Garrity (Michigan State University), Frank Larimer (Oak Ridge National Laboratory), Camilla Nesb (Dalhousie University), and Paul Richardson (Joint Genome Institute). Participants are encouraged to informally share their views and results.

Dr. George Garrity Carolus Linneaus in the postgenomic era

This discussion will focus on a problem that plagues us all to some degree or another - biological nomenclature. Ideally, our formalized system of nomenclature is supposed to improve communication among biologists. In reality, it seems to be a major obstacle, especially when misapplied. Although the problem is evident in the literature, it is most severe in the sequence databases, which now serve as the principal source and repository of data used in comparative biology. Moreover, the sequence databases tend to propagate such errors for a variety of reasons. As biological data proliferates and interconnects, it depends increasingly on software infrastructure, and it becomes increasingly obvious that biological names do not meet the requirements of a good identifier, in strict computing terms. A good identifier should be unique and persistent. As an outgrowth of my current DOE funded project, we have been exploring a practical and workable solution that we believe will help solve the problem in a future-proof fashion.

Dr. Frank Larimer Comparative Genomics of Microbial Photoautotrophs & Relatives

Dr. Camilla Nesb - Comparative Genomics: What to do? Some simple methods"

Comparative approaches including: suppressive subtractive hybridization; sequencing strain-specific loci on lambda clones identified by hybridization to subtraction clones; Long - walk PCR from conserved genes; and BAC cloning of environmental DNA will be discussed. Examples using the genus Thermotogales with the genome sequence of Thermotoga maritima MSB8 as the reference will be provided.

Dr. Paul Richardson - "The genome sequence of Ciona intestinalis offers clues to vertebrate origins." The whole genome sequencing strategy for Ciona will be described, as will methods used to identify genes. Comparisons of selected gene families found in Ciona with those of other chordates and vertebrates will also be described.

Speaker Contact Information

Dr. George M Garrity
Bergey's Manual Trust
152 Giltner Hall
Dept of Micro/MI State Univ
East Lansing, MI 48824-1101
Business Phone: 517 432 2459
Fax Number: 517 432 2458
Email Address: garrity@pilot.msu.edu

Dr. Frank Larimer
ORNL
Voice: 865-574-1253
Email Address: larimerfw@ornl.gov

Dr. Camilla Lothe Nesb,
Department of Biochemistry & Molecular Biology
Dalhousie University
5850 College Street
Halifax, Nova Scotia
Canada B3H 1X5
phone: (+1) 902 494 2968
fax: (+1) 902 494 1355
E-mail: cnesbo@dal.ca

Dr. Paul Richardson
DOE Joint Genome Institute
2800 Mitchell Drive, B100
Walnut Creek, CA 94598 USA
PH: 925.296.5797
Cell: 925.980.4648
FAX: 925.296.5875
e-mail: pmricharson@lbl.gov

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