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Physical mapping of complex genomes by sampled sequencing: a theoretical analysis
K Kupfer1, M W Smith, J Quackenbush
1McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas 75235-8591, USA.
Genomics
|May 1, 1995
Summary
Genomic Sequence Sampling (GSS) offers high-resolution physical mapping of complex genomes by assembling cosmid contigs and sequencing ends. This method achieves detailed physical maps with high sequence recovery and accuracy.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- High-throughput, high-resolution physical mapping is crucial for complex genomes.
- Existing methods may have limitations in resolution and efficiency.
Purpose of the Study:
- To determine theoretical parameters for Genomic Sequence Sampling (GSS) mapping.
- To evaluate the effectiveness of the GSS contig-building strategy.
- To calculate the expected fraction of target genome recovered as mapped sequence.
Main Methods:
- Genomic Sequence Sampling (GSS) utilizes high-density cosmid contig assembly over large genomic regions.
- DNA sequencing of cosmid ends provides sequence fragments.
- A novel strategy determines insert orientation for high-resolution mapping.
- Algorithm involves restriction digestion, fragment matching for contig assembly, and end-orientation.
Main Results:
- GSS generates physical maps with 1- to 5-kb resolution.
- The method achieves a substantial portion of the entire sequence at one-pass accuracy.
- The contig-building strategy's effectiveness is evaluated.
Conclusions:
- GSS is a viable method for high-throughput, high-resolution physical mapping of complex genomes.
- The orientation determination enhances mapping precision.
- The study provides theoretical parameters and assesses sequence recovery potential.