Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments
Abstract
We construct several score functions for use in locating unusually conserved regions in a genome-wide search of aligned DNA from two species. We test these functions on regions of the human genome aligned to the mouse genome. These score functions are derived from properties of neutrally evolving sites on the mouse and human genome, and can be adjusted to the local background rate of conservation. The aim of these functions is to try to identify regions of the human genome that are conserved by evolutionary selection, because they have an important function, rather than by chance. We use them to get a very rough estimate of the amount of DNA in the human genome that is under selection.
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The vertebrate coverage is similar to recent estimates of 5%-8% for the share of the human genome under purifying selection.
“Note that the vertebrate coverage is similar to recent estimates of 5%-8% for the share of the human genome that is under purifying selection”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Roskin et al. 2003
The composition of vertebrate conserved elements agrees with bulk statistical estimates of the share of the human genome under selection and with an analysis of conserved elements in the CFTR region.
“These numbers are in good agreement both with bulk statistical estimates, based on genome-wide human/mouse and human/ mouse/rat alignments, of the share of the human genome that is under selection (Chiaromonte et al. 2003;Roskin et al. 2003;Cooper et al. 2004), and with an analysis of conserved elements in the region of the CFTR gene (Margulies et al. 2003;Thomas et al. 2003).”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Roskin et al. 2003
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
Self-citationEvaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Pervez, M. T., Babar, M. E., Nadeem, A., Aslam, M., Awan, A. R., Aslam, N., Hussain, T., Naveed, N., Qadri, S., Waheed, U., et al. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s19199 · Cited by 48 · see citing works
- Authors
- Roskin, K. M., Diekhans, M., & Haussler, D.
- Affiliations
- Università Cattolica del Sacro Cuore (IT)
- Venue
- Proceedings of the seventh annual international conference on Research in computational molecular biology
- Publisher
- ACM
- Published
- 2003-04-10
- Pages
- 257-266
- OpenAlex
- W2045221040
- Cited by
- 14
- References
- 0
- Citations by year
- 2015: 1 · 2014: 2
- FWCI
- 6.43
- Type
- conference paper
- Language
- en
- Open access
- closed
- Locations
- Research in Computational Molecular Biology (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- conserved domains, positive selection, neutral evolution
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