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The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
  • P. Sharp, W. Li
  • Biology, Medicine
  • Nucleic acids research
  • 11 February 1987
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed, useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons ofCodon usage in different organisms. Expand
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites. Expand
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of allExpand
Origins of HIV and the AIDS pandemic.
  • P. Sharp, B. Hahn
  • Biology, Medicine
  • Cold Spring Harbor perspectives in medicine
  • 1 September 2011
Tracing the genetic changes that occurred as SIVs crossed from monkeys to apes and from apes to humans provides a new framework to examine the requirements of successful host switches and to gauge future zoonotic risk. Expand
Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes
The genome of a new SIVcpz strain is sequenced and the subspecies identity of all known SIV cpz-infected chimpanzees is determined, by mitochondrial DNA analysis, and it is found that two chimpanzee subspecies in Africa harbour SIVCPz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. Expand
AIDS as a zoonosis: scientific and public health implications.
Evidence of simian immunodeficiency virus (SIV) infection has been reported for 26 different species of African nonhuman primates and the implications of human infection by a diverse set of SIVs and of exposure to a plethora of additional human immunodewirable viruses are discussed. Expand
Evidence for two independent domestications of cattle.
Application of a molecular clock suggests that the two major mtDNA clades diverged at least 200,000, and possibly as much as 1 million, years ago, as evidence for two separate domestication events of different subspecies of the aurochs, Bos primigenius and Bos taurus. Expand
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.
The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined, and data discussed are consistent with the effects of translational selection among synonymous codons, as seen in unicellular organisms. Expand
Fast and sensitive multiple sequence alignments on a microcomputer
A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. Expand
HIV-1 Nomenclature Proposal
A clear and consistent genetic classification of human immunodeficiency virus-type 1 (HIV-1) strains continues to be of great utility in epidemiological tracking of the AIDS pandemic and in vaccineExpand