4.8 Article

Fast algorithms for large-scale genome alignment and comparison

Journal

NUCLEIC ACIDS RESEARCH
Volume 30, Issue 11, Pages 2478-2483

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/nar/30.11.2478

Keywords

-

Funding

  1. NLM NIH HHS [R01 LM006845, R01-LM06845] Funding Source: Medline
  2. PHS HHS [R01-A142243] Funding Source: Medline

Ask authors/readers for more resources

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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.8
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available