 |
A two-phase approach for detecting recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. In: S. Hazelhurst and M. Ramsay, Proceedings of The First Southern African Bioinformatics Workshop. The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, (9-16). 28-30 January, 2007.
|
|
| |
| Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials) |
| Name |
Description |
MIMEType |
Size |
Downloads |
ChanCX_SABioinf.pdf
|
Full text of the conference paper |
application/pdf |
148.11KB |
51 |
|
cxc_sabio_07.pdf
|
Conference paper |
application/pdf |
281.11KB |
10 |
| Author(s) |
Chan, Cheong Xin
Beiko, Robert G.
Ragan, Mark A.
|
| Title of paper |
A two-phase approach for detecting recombination in nucleotide sequences
|
| Conference name |
The First Southern African Bioinformatics Workshop
|
| Conference location |
Johannesburg, South Africa
|
| Conference dates |
28-30 January, 2007
|
| Proceedings title |
Proceedings of The First Southern African Bioinformatics Workshop
|
| Editor(s) |
S. Hazelhurst
M. Ramsay
|
| Place published |
Johannesburg, South Africa
|
| Publisher |
University of the Witwatersrand
|
| Publication date |
2007
|
| Start page |
9
|
| End page |
16
|
| Language |
eng
|
| Abstract/Summary |
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.
|
| Subjects |
270200 Genetics
279900 Other Biological Sciences
239901 Biological Mathematics
|
| Keyword(s) |
comparative genomics
recombination detection
sequence analysis
evolution and phylogenetics
|
|
|
|
