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Genome Sequence Assembly:Algorithms and Issues
July 2002 (vol. 35 no. 7)
pp. 47-54
Mihai Pop, Institute for Genomics Research
Steven L. Salzberg, Institute for Genomic Research
Martin Shumway, Institute for Genomic Research

Ultimately, genome sequencing seeks to provide an organism's complete DNA sequence. Automation of DNA sequencing allowed scientists to decode entire genomes and gave birth to genomics, the analytic and comparative study of genomes. Although genomes can include billions of nucleotides, the chemical reactions researchers use to decode the DNA are accurate for only about 600 to 700 nucleotides at a time.

The DNA reads that sequencing produces must then be assembled into a complete picture of the genome. Errors and certain DNA characteristics complicate assembly. Resolving these problemsentails an additional and costly finishing phase that involves extensive human intervention. Assembly programs can dramatically reduce this cost by taking into account additional informationobtained during finishing. Algorithms that can assemble millions of DNA fragments into gene sequences underlie the current revolution in biotechnology, helping researchers build the growingdatabase of complete genomes.

Mihai Pop, Steven L. Salzberg, Martin Shumway, "Genome Sequence Assembly:Algorithms and Issues," Computer, vol. 35, no. 7, pp. 47-54, July 2002, doi:10.1109/MC.2002.1016901
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