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This project is collaborated between The Forsyth Institute (TFI) and The Institute for Genomic Research (TIGR), and is funded by National Institute of Dental and Craniofacial Research (NIDCR)


The accepted approach for sequencing large segments of DNA (>100 kb) has been to spend substantial effort in the development of lambda or cosmid libraries and their subsequent mapping. Developing approaches for rapid and efficient sequencing and assembly of large segments of DNA is critical for genome sequencing projects. We have developed a whole genome sequencing approach based on a Lander-Waterman model of shotgun sequencing that reduces the need for "top down" efforts. In collaboration with Hamilton Smith's laboratory at Johns Hopkins University, we first demonstrated the value of this whole genome shotgun approach to the complete sequencing of the 1,830,140 bp genome of Haemophilus influenzae (Fleischmann et al., 1995).

Completion of the sequencing of the 1.83 Mb chromosome of H. influenzae resulted in the integration a variety of parameters necessary for high throughput and cost efficient sequencing and analysis of megabase regions of genomic DNA. The practicality of a predominantly random approach was examined with respect to: 1) optimal size of randomly sheared genomic fragments; 2) sufficient number and randomization of clones to cover the vast majority of the genome with sufficient redundancy to give highly accurate sequence; 3) the effectiveness of enhanced read lengths in overcoming the problems of contig formation between clones containing repetitive sequences; 4) minimizing the number of gap closure reactions; 5) evaluating and developing software capability to efficiently assemble and manage megabase segments of genomic DNA; and 6) the ability to bring the per bp cost of finished genomic DNA sequence to below $0.50 per bp.

This page is created and maintained by Drs. Margaret Duncan, Floyd Dewhirst, and Tsute Chen, Department of Molecular Genetics, The Forsyth Institute .

Last modified on 02/20/2002

Copyright 2000, 2001, 2002 by The Forsyth Institute