Novos horizontes para os genomas

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DOE/SC-0071

New Horizons in Genomics
U.S. Department of Energy Joint Genome Institute

Santa Fe, New Mexico March 30-April 1, 2003

Prepared for the Joint Genome Institute U.S. Department of Energy Office of Science Office of Biological and Environmental Research JGI Production Genomic Facility 2800 Mitchell Drive Walnut Creek, CA 94598

Prepared by Human Genome Management InformationSystem 1060 Commerce Park Oak Ridge National Laboratory Oak Ridge, TN 37830 Managed by UT-Battelle, LLC For the U.S. Department of Energy Under contract DE-AC05-00OR22725

Contents
New Horizons in Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Sequencing Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1

Plasmidomics: CloningNaturally Occurring Plasmids for Sequencing and Functional Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Anne Marie Erler, Patricia Sobecky, Gary L. Andersen, and Peter Agron

2

Shotgun Library Utilization for Sequencing Projects at the JGI . . . . . . . . . . 3
Chris Detter, Eileen Dalin, Jamie M. Jett, Doug Smith, Jenna Morgan, Hope Tice,Saima Shams, Corey Chinn, Eddy Rubin, and Paul M. Richardson

3

BAC Libraries for Whole-Genome Sequencing, Comparative Genomics and Haplotype Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Pieter J. de Jong, Baoli Zhu, Mikhail Nefedov, Chung-Li Shu, Yuko Yoshinaga, and Kazutoyo Osoegawa

4

Using Transposons to Resolve Repeats in BAC Clones . . .. . . . . . . . . . . . . . 5
Jamie Jett, Jeremy Schmutz, Eileen Dalin, Jane Grimwood, Corey Chinn, Doug Smith, Susan Lucas, Chris Detter, Paul Richardson, and Eddy Rubin

5

Single Molecule DNA Sequence Profiling In Zero-Mode Waveguides Using -Phosphate Linked Nucleotide Analogs . . . . . . . . . . . . . . . . . . . . . . . 5
Jonas Korlach, Michael Levene, Mathieu Foquet, Stephen W.Turner, Harold G. Craighead, and Watt W. Webb

6

Complete Direct Sequencing of BAC, Phage and Microbial Genomes using ThermoFidelase, Fimer and D-Strap Technologies . . . . . . . . . . . . . . . 6
S. Kozyavkin, O. Shcherbinina, V. Shakhova, N. Pavlova, A. Morocho, V. Karamychev, Y. Malykh, A. Pavlov, N. Polouchine, A. Malykh, and A. Slesarev

7

Isolation of Exceptional Chromosomal Regions toClose the Gaps in the Draft Human Genome Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
S.-H. Leem, N. Kouprina, and V. Larionov

New Horizons in Genomics

iii

8

pFOS-LA: A Modified Vector for Production of Random Shear Fosmid Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
J. Longmire, N.Brown, S. Malfatti, Jack Meeks, and Patrick Chain

9

Using YACs to Close Gaps at the JGI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Jenna Morgan, Duncan Scott, Joel Martin, Tijana Glavina, Susan Lucas, Chris Detter, Paul Richardson, and Eddy Rubin

10

Helix-Hairpin-Helix Motifs to Create Processive, Hyperstable and Inhibitor-Resistant Enzymes. . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . 9
Alexei Slesarev, Andrey Pavlov, Nadya Pavlova, and Sergei Kozyavkin

11 12

Efficient Isothermal Amplification of Single DNA Molecules . . . . . . . . . . . 10
Stanley Tabor and Charles Richardson

Improved DENS: Finishing Without Custom Primers—From Human to Microbes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . 11
Olga Chertkov, Marie-Claude Krawczyk, Mira Dimitrijevic-Bussod, David Bruce, Mark Mundt, Paul Gilna, Norman Doggett, and Levy Ulanovsky

Systems Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

13

New Methods and Models for Genomic Systems Biology . . . . . . . . . . . . . . 13
George Church, Martin Steffen,...
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