Resolution effects in reconstructing ancestral genomes
Abstract Background The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. Results We use the median reconstruction at the synteny block level...
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doaj-6be1c16ad13c4482b3b3765e543d78172020-11-25T00:30:00ZengBMCBMC Genomics1471-21642018-05-0119S2515910.1186/s12864-018-4462-yResolution effects in reconstructing ancestral genomesChunfang Zheng0Yuji Jeong1Madisyn Gabrielle Turcotte2David Sankoff3Department of Mathematics and Statistics, University of OttawaDepartment of Mathematics and Statistics, University of OttawaDepartment of Mathematics and Statistics, University of OttawaDepartment of Mathematics and Statistics, University of OttawaAbstract Background The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. Results We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. Conclusions We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.http://link.springer.com/article/10.1186/s12864-018-4462-yGranularityGentianalesGene orderMedianSynteny blocksRearrangements |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chunfang Zheng Yuji Jeong Madisyn Gabrielle Turcotte David Sankoff |
spellingShingle |
Chunfang Zheng Yuji Jeong Madisyn Gabrielle Turcotte David Sankoff Resolution effects in reconstructing ancestral genomes BMC Genomics Granularity Gentianales Gene order Median Synteny blocks Rearrangements |
author_facet |
Chunfang Zheng Yuji Jeong Madisyn Gabrielle Turcotte David Sankoff |
author_sort |
Chunfang Zheng |
title |
Resolution effects in reconstructing ancestral genomes |
title_short |
Resolution effects in reconstructing ancestral genomes |
title_full |
Resolution effects in reconstructing ancestral genomes |
title_fullStr |
Resolution effects in reconstructing ancestral genomes |
title_full_unstemmed |
Resolution effects in reconstructing ancestral genomes |
title_sort |
resolution effects in reconstructing ancestral genomes |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-05-01 |
description |
Abstract Background The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. Results We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. Conclusions We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics. |
topic |
Granularity Gentianales Gene order Median Synteny blocks Rearrangements |
url |
http://link.springer.com/article/10.1186/s12864-018-4462-y |
work_keys_str_mv |
AT chunfangzheng resolutioneffectsinreconstructingancestralgenomes AT yujijeong resolutioneffectsinreconstructingancestralgenomes AT madisyngabrielleturcotte resolutioneffectsinreconstructingancestralgenomes AT davidsankoff resolutioneffectsinreconstructingancestralgenomes |
_version_ |
1725328519668432896 |