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PMID: 21393387 Published · ppublish English Comparative Study Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes.

Genome research ·Vol. 21 ·No. 6 ·2011-06-00 ·Pages 863-74

Markova-Raina P, Petrov D

Abstract

We investigate the effect of aligner choice on inferences of positive selection using site-specific models of molecular evolution. We find that independently of the choice of aligner, the rate of false positives is unacceptably high. Our study is a whole-genome analysis of all protein-coding genes in 12 Drosophila genomes annotated in either all 12 species (~6690 genes) or in the six melanogaster group species. We compare six popular aligners: PRANK, T-Coffee, ClustalW, ProbCons, AMAP, and MUSCLE, and find that the aligner choice strongly influences the estimates of positive selection. Differences persist when we use (1) different stringency cutoffs, (2) different selection inference models, (3) alignments with or without gaps, and/or additional masking, (4) per-site versus per-gene statistics, (5) closely related melanogaster group species versus more distant 12 Drosophila genomes. Furthermore, we find that these differences are consequential for downstream analyses such as determination of over/under-represented GO terms associated with positive selection. Visual analysis indicates that most sites inferred as positively selected are, in fact, misaligned at the codon level, resulting in false positive rates of 48%-82%. PRANK, which has been reported to outperform other aligners in simulations, performed best in our empirical study as well. Unfortunately, PRANK still had a high, and unacceptable for most applications, false positives rate of 50%-55%. We identify misannotations and indels, many of which appear to be located in disordered protein regions, as primary culprits for the high misalignment-related error levels and discuss possible workaround approaches to this apparently pervasive problem in genome-wide evolutionary analyses.

MeSH Terms
Animals Drosophila/genetics Evolution, Molecular False Positive Reactions Genome/genetics Genomics/methods Selection, Genetic Sequence Alignment/methods Software Species Specificity
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Markova-Raina Penka
Department of Biology, Stanford University, Stanford, California 94305, USA. [email protected]
Petrov Dmitri
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.115949.110
Email
[email protected]
Published
2011-06-00
Epub
2011-00-10
Pages
863-74
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3106319
Subset
IM
Grants
NIGMS NIH HHS · GM089926 · United States
NLM NIH HHS · T5 LM07033 · United States
NIGMS NIH HHS · T32 GM63495 · United States
NLM NIH HHS · T15 LM007033 · United States
NIGMS NIH HHS · T32 GM063495 · United States
NIGMS NIH HHS · R01 GM089926 · United States
NHGRI NIH HHS · P50 HG002568 · United States
NIGMS NIH HHS · R01 GM077368 · United States
NHGRI NIH HHS · HG002568-07 · United States
NIGMS NIH HHS · GM077368 · United States
External Links
PubMed source DOI: 10.1101/gr.115949.110 PMC Full Text View journal details
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