PMID- 16256279
OWN - NLM
STAT- MEDLINE
DCOM- 20060428
LR  - 20091119
IS  - 0378-1119 (Print)
IS  - 0378-1119 (Linking)
VI  - 365
DP  - 2006 Jan 3
TI  - Statistical properties of the methods for detecting positively selected amino 
      acid sites.
PG  - 125-9
AB  - Parsimony and Bayesian methods have been developed for detecting positively 
      selected amino acid sites. It has been reported that the parsimony method is 
      generally conservative. In contrast, the Bayesian method is known to identify 
      more positively selected sites than the parsimony method, especially when the 
      number of sequences analyzed is small, although the interpretation of results 
      obtained from the former method is controversial. Here I show that the 
      likelihood-ratio test (LRT) of the Bayesian method corresponds to the parsimony 
      method with window analysis, by analyzing the nucleotide sequences encoding the 
      trans-activator (tax) gene of human T-cell lymphotropic virus type I (HTLV-I). It 
      is also indicated that in the parsimony method, the test of selective neutrality 
      using the binomial probability tends to be conservative, but the Monte Carlo 
      simulation is useful for solving this problem. In addition, in the Bayesian 
      method, the bootstrap method appears to produce similar results to the LRT. This 
      information may be useful for improving the methods for detecting positively 
      selected amino acid sites.
FAU - Suzuki, Yoshiyuki
AU  - Suzuki Y
AD  - Center for Information Biology and DNA Data Bank of Japan, National Institute of 
      Genetics, Mishima-shi, Shizuoka-ken 411-8540, Japan. yossuzuk@lab.nig.ac.jp
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20051026
PL  - Netherlands
TA  - Gene
JT  - Gene
JID - 7706761
RN  - 0 (Amino Acids)
RN  - 0 (Codon)
RN  - 0 (Gene Products, tax)
SB  - IM
MH  - Amino Acid Sequence
MH  - Amino Acids/*genetics
MH  - Base Sequence
MH  - Bayes Theorem
MH  - Binding Sites
MH  - Codon
MH  - Computer Simulation
MH  - Databases, Factual
MH  - Gene Products, tax/*chemistry
MH  - Human T-lymphotropic virus 1/*genetics
MH  - Humans
MH  - *Likelihood Functions
MH  - Molecular Sequence Data
MH  - Monte Carlo Method
MH  - Phylogeny
MH  - *Selection, Genetic
MH  - Sequence Homology, Amino Acid
MH  - Statistics as Topic
EDAT- 2005/11/01 09:00
MHDA- 2006/04/29 09:00
CRDT- 2005/11/01 09:00
PHST- 2005/04/28 00:00 [received]
PHST- 2005/06/30 00:00 [revised]
PHST- 2005/09/07 00:00 [accepted]
PHST- 2005/11/01 09:00 [pubmed]
PHST- 2006/04/29 09:00 [medline]
PHST- 2005/11/01 09:00 [entrez]
AID - S0378-1119(05)00535-4 [pii]
AID - 10.1016/j.gene.2005.09.002 [doi]
PST - ppublish
SO  - Gene. 2006 Jan 3;365:125-9. doi: 10.1016/j.gene.2005.09.002. Epub 2005 Oct 26.