Fast algorithms for large-scale genome alignment and comparison

Arthur L. Delcher, Adam Phillippy, Jane Carlton, Steven L. Salzberg

Research output: Contribution to journalArticle

Abstract

We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has been used successfully to align the entire human and mouse genomes to each other, and to align numerous smaller eukaryotic and prokaryotic genomes. A new module permits the alignment of multiple DNA sequence fragments, which has proven valuable in the comparison of incomplete genome sequences. We also describe a method to align more distantly related genomes by detecting protein sequence homology. This extension to MUMmer aligns two genomes after translating the sequence in all six reading frames, extracts all matching protein sequences and then clusters together matches. This method has been applied to both incomplete and complete genome sequences in order to detect regions of conserved synteny, in which multiple proteins from one organism are found in the same order and orientation in another. The system code is being made freely available by the authors.

Original languageEnglish (US)
Pages (from-to)2478-2483
Number of pages6
JournalNucleic Acids Research
Volume30
Issue number11
StatePublished - Jun 1 2002

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Genome
Synteny
Amino Acid Sequence Homology
Reading Frames
Human Genome
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Delcher, A. L., Phillippy, A., Carlton, J., & Salzberg, S. L. (2002). Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research, 30(11), 2478-2483.

Fast algorithms for large-scale genome alignment and comparison. / Delcher, Arthur L.; Phillippy, Adam; Carlton, Jane; Salzberg, Steven L.

In: Nucleic Acids Research, Vol. 30, No. 11, 01.06.2002, p. 2478-2483.

Research output: Contribution to journalArticle

Delcher, AL, Phillippy, A, Carlton, J & Salzberg, SL 2002, 'Fast algorithms for large-scale genome alignment and comparison', Nucleic Acids Research, vol. 30, no. 11, pp. 2478-2483.
Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research. 2002 Jun 1;30(11):2478-2483.
Delcher, Arthur L. ; Phillippy, Adam ; Carlton, Jane ; Salzberg, Steven L. / Fast algorithms for large-scale genome alignment and comparison. In: Nucleic Acids Research. 2002 ; Vol. 30, No. 11. pp. 2478-2483.
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