|
|
ReportsAlignment Uncertainty and Genomic AnalysisThe statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions.
1 Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA. * To whom correspondence should be addressed. E-mail: johnh{at}berkeley.edu
The editors suggest the following Related Resources on Science sites:In Science Magazine
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
|
Magazine | News | Signaling | Careers | Multimedia | Collections | Help | Site Map | RSS
Subscribe | Feedback | Privacy / Legal | About Us | Advertise With Us | Contact Us
© 2008 American Association for the Advancement of Science. All Rights Reserved.
AAAS is a partner of HINARI, AGORA, PatientInform, CrossRef, and COUNTER.
You have reached the bottom of the page. Back to top