Genome sequence assembly: Algorithms and issues

Mihai Pop, Steven L. Salzberg, Martin Shumway

Research output: Contribution to journalArticlepeer-review

Abstract

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 problems entails an additional and costly finishing phase that involves extensive human intervention. Assembly programs can dramatically reduce this cost by taking into account additional information obtained during finishing. Algorithms that can assemble millions of DNA fragments into gene sequences underlie the current revolution in biotechnology, helping researchers build the growing database of complete genomes.

Original languageEnglish (US)
Pages (from-to)47-54
Number of pages8
JournalComputer
Volume35
Issue number7
DOIs
StatePublished - Jul 2002
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science(all)

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