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An intermediate grade of finished genomic sequence suitable for comparative analyses
Robert W Blakesley1, Nancy F Hansen, James C Mullikin
1NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Genome Research
|October 14, 2004
Summary
Generating high-quality genomic sequence for comparisons is now affordable. Comparative-grade finished sequence offers a cost-effective solution for multispecies analysis, significantly reducing reagent and personnel costs.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Genomic sequence finishing is crucial but expensive.
- High-quality finished sequence is not cost-justified for large-scale projects.
Purpose of the Study:
- To describe the generation and quality of comparative-grade finished sequence.
- To provide a cost-effective alternative for multispecies genomic comparisons.
Main Methods:
- Generation of intermediate-grade finished genomic sequence.
- Quality assessment of the comparative-grade sequence.
- Comparison of resource requirements with near-perfect finished sequence.
Main Results:
- Comparative-grade sequence is high quality, with 99% of total sequence represented.
- Residual gaps and errors are mainly in repetitive elements.
- Requires 40-fold less reagents and 10-fold less personnel effort than near-perfect finishing.
Conclusions:
- Comparative-grade sequence finishing is a practical and affordable option.
- This method is suitable for multispecies sequence comparisons.
- Potential application to whole-genome shotgun sequencing projects.