Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

Aaron C.E. Darling; Bob Mau; Frederick R. Blattner; Nicole T. Perna

doi:10.1101/gr.2289704

journal article Open Access Jul 01, 2004

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

Aaron C.E. Darling Bob Mau Frederick R. Blattner Nicole T. Perna

Genome Research Vol. 14 No. 7 pp. 1394-1403 · Cold Spring Harbor Laboratory

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Abstract

As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.

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Details

Published: Jul 01, 2004
Vol/Issue: 14(7)
Pages: 1394-1403

Authors

Frederick R. Blattner

F. R. Blattner, G. Plunkett III, N. T. Perna, J. D. Glasner, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao are at the Laboratory of Genetics, University of Wisconsin–Madison, 445 Henry Mall, Madison, WI 53706, USA. C. A. Bloch and C. K. Rode are in the Department of Pediatrics, University of Michigan School of Medicine, 1150 West Medical Center Drive, Ann Arbor, MI 48105, USA. V. Burland is at FMC Bioproducts, 191 Thomaston Street, Rockland,...

N

Nicole T. Perna

Cite This Article

Aaron C.E. Darling, Bob Mau, Frederick R. Blattner, et al. (2004). Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Genome Research, 14(7), 1394-1403. https://doi.org/10.1101/gr.2289704

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

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