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Algorithmic challenges in mammalian whole-genome assembly

Part 4. Bioinformatics

4.1. Genome Assembly and Sequencing

Specialist Review

  1. Serafim Batzoglou

Published Online: 15 JAN 2005

DOI: 10.1002/047001153X.g401201

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Batzoglou, S. 2005. Algorithmic challenges in mammalian whole-genome assembly. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.1:2.

Author Information

  1. Stanford University, Stanford, CA, USA

Publication History

  1. Published Online: 15 JAN 2005

Abstract

Sequencing of the human, mouse, and rat genomes was accomplished more quickly than had seemed feasible a mere eight years ago. The accelerating pace of sequencing has been made possible by the development of large-scale laboratory operations, assembly algorithms, and less so by changes in the underlying sequencing technologies. This short review summarizes the computational challenges of whole-genome assembly and the algorithms and software systems that enabled the recent advances in sequencing of mammalian genomes.

Keywords:

  • DNA sequencing;
  • whole-genome shotgun assembly;
  • physical mapping;
  • contig;
  • scaffold;
  • overlap-layout-consensus