Summary
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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References
Dewey, C. N. (2006) Whole-genome alignments and polytopes for comparative genomics. Ph.D. thesis, University of California, Berkely.
Bray, N. and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693–699.
Dewey, C. N. and Pachter, L. (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum. Mol. Genet. 15, R51–R56.
Karolchik, D., Baertsch, R., Diekhans, M., et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51–54.
Smit, A. F., Hubley, R., and Green, P. (1996-2004) RepeatMasker Open-3.0. http://www.repeatmasker.org.
Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580.
Korf, I. (2004) Gene finding in novel genomes. BMC Bioinformatics 5, 59.
Kent, W. J. (2002) BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664.
Guigo, R. (1998) Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol. 5, 681–702.
Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94.
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.
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Dewey, C.N. (2007). Aligning Multiple Whole Genomes with Mercator and MAVID. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_14
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DOI: https://doi.org/10.1007/978-1-59745-514-5_14
Publisher Name: Humana Press
Print ISBN: 978-1-58829-693-1
Online ISBN: 978-1-59745-514-5
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