Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Open accessAbstract
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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Anchor-based methods use a set of anchor sequences, typically a subset of the input sequences, to guide the alignment of the remaining sequences in the dataset.
“Anchor-based methods use a set of anchor sequences, which are typically a subset of the input sequences, to guide the alignment of the remaining sequences in the dataset [27].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [27]
The Methods section defines Mauve’s anchors as matching subsequences (multi-MUMs) shared by genomes, not as a subset of the input sequences. The paper does say those anchors guide subsequent alignment, but its description contradicts the claim’s characterization of what the anchors are. (LLM, conf=0.87)
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Experimental — accuracy not yet measuredSome algorithms, like Mauve and Progressive Cactus, have built-in features for handling genomic rearrangements.
“Some algorithms, like Mauve and Progressive Cactus, have built-in features for handling these rearrangements [27].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [27]
The Abstract says Mauve was developed to align genomic DNA in the presence of rearrangements, and the Methods describe its breakpoint-elimination algorithm for noncollinear anchoring. Our copy does not address Progressive Cactus, so it supports the claim about Mauve but not the claim about both algorithms. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMauve can identify entire similar regions between a set of genomes, such as rearrangements, translocations, and inversions, and the exact breakpoints of each rearrangement across multiple genomes.
“Mauve is a genome alignment method which is able to identify entire similar regions between a set of genomes, such as rearrangements, translocation, and inversions, and the exact breakpoints of each rearrangement across multiple genomes [27].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [27]
Other algorithms may require additional steps or tools to correctly align regions with genomic rearrangements.
“Other algorithms may require additional steps or tools to correctly align regions with genomic rearrangements [27].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [27]
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- Authors
- Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T.
- Affiliations
- University of Wisconsin–Madison (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-07
- Volume
- 14
- Issue
- 7
- Pages
- 1394-1403
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC442156
- OpenAlex
- W7095603021
- Cited by
- 4,949
- References
- 1
- Citations by year
- 2026: 270 · 2025: 375 · 2024: 443 · 2023: 389 · 2022: 438 · 2021: 405 · 2020: 420 · 2019: 367 · 2018: 280 · 2017: 286 · 2016: 245 · 2015: 189 · 2014: 181 · 2013: 139 · 2012: 133
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- OPUS - Open Publications of UTS Scholars (University of Technology Sydney) (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM62994-02, R01GM062994)
- U.S. National Library of Medicine (T15LM007359)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- multiple sequence alignment, genome rearrangement, comparative genomics, sequence alignment software
- MeSH terms
- Chromosomes, Bacterial, Computer Simulation, DNA, Bacterial, Enterobacteriaceae, Escherichia coli, Recombination, Genetic, Salmonella typhi, Salmonella typhimurium, Shigella flexneri, Software, Software Design, Software Validation, Species Specificity, Sequence Alignment, Genome, Bacterial, Conserved Sequence, Escherichia coli O157
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