Aligning Multiple Whole Genomes with Mercator and MAVID
Abstract
The availability of an increasing number of whole genome sequences presents us with the need for tools to quickly put them into a nucleotide-level multiple alignment. Mercator and MAVID are two programs that can be combined to accomplish this task. Given multiple whole genomes as input, Mercator is first used to construct an orthology map, which is then used to guide nucleotide-level multiple alignments produced by MAVID. These programs are both fast and freely available, allowing researchers to perform genome alignments on a single laptop. This tutorial will guide the researcher through the steps required for whole-genome alignment with Mercator and MAVID.
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Memory usage determines the size of genomes or datasets that the algorithm can handle at once.
“Memory usage determines the size of genomes or datasets that the algorithm can handle at once [45].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [45]
Cites
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848 · see citing works
Aken, B. L., Achuthan, P., Akanni, W., Amode, M. R., Bernsdorff, F., Bhai, J., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1104 · Cited by 512 · see citing works
Whole-Genome Alignment: Methods, Challenges, and Future Directions
Saada, B., Zhang, T., Siga, E., Zhang, J., & Magalhães Muniz, M. M. (2024) · Applied Sciences · doi:10.3390/app14114837 · Cited by 15 · see citing works
- Authors
- Dewey, C. N.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Dewey, Colin N.
- ORCID
- Dewey, Colin N.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2007
- Volume
- 395
- Pages
- 221-235
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2412439129
- Cited by
- 86
- References
- 1
- Citations by year
- 2024: 1 · 2023: 1 · 2020: 7 · 2019: 4 · 2018: 4 · 2017: 1 · 2016: 6 · 2015: 6 · 2014: 6 · 2013: 9 · 2012: 8
- FWCI
- 9.18
- Type
- book chapter
- Language
- en
- Open access
- closed
- Locations
- Methods in molecular biology (publishedVersion)
- PubMed (publishedVersion)
- 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
- whole-genome alignment, Mercator, comparative genomics, orthologs
- MeSH terms
- Sequence Alignment, Genome, Internet, Databases, Genetic
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