Cactus: Algorithms for genome multiple sequence alignment
Open accessAbstract
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new “Cactus” alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
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Cactus is a reference-free multiple genome alignment program that has been shown to be highly accurate.
“Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [6]
Cactus has neither of these restrictions; it can generate a reference-free multiple alignment that allows detection of multiple-orthology relationships.
“Cactus6 is a genome alignment program that has neither of these restrictions; it can generate a reference-free multiple alignment that allows the detection of multiple-orthology relationships.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [6]
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“conservation of the reference sequence (Siepel et al. 2005), but its construction is inherently biased,making it less useful for studying the relationships betweennon-reference species in the alignments.”
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Research works printed but not linked: 5
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Self-citationProgressive Cactus is a multiple-genome aligner for the thousand-genome era
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- Authors
- Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., & Haussler, D.
- Affiliations
- University of California, Santa Cruz (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-06-10
- Volume
- 21
- Issue
- 9
- Pages
- 1512-1528
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3166836
- OpenAlex
- W2166825456
- Cited by
- 243
- References
- 1
- Citations by year
- 2026: 11 · 2025: 13 · 2024: 18 · 2023: 16 · 2022: 19 · 2021: 16 · 2020: 40 · 2019: 26 · 2018: 29 · 2017: 11 · 2016: 10 · 2015: 11 · 2014: 12 · 2013: 5 · 2012: 5
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Genome Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- European Bioinformatics Institute
- National Institutes of Health (5u54hg004555-04)
- National Human Genome Research Institute (U01HG004695, U54-HG004555, P41HG002371, U41HG004568)
- 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, cactus graphs, genome alignment, rearrangement, copy number variation, gene duplication, alignment optimization, primates
- MeSH terms
- Algorithms, Animals, Computer Simulation, Humans, Primates, Software, Sequence Alignment, Sequence Analysis, DNA, Genomics, Mice
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