The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
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.
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
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.
Origins of HIV and the AIDS pandemic.
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.
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.
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.
Evidence for two independent domestications of cattle.
- R. Loftus, D. MacHugh, D. Bradley, P. Sharp, P. Cunningham
- BiologyProceedings of the National Academy of Sciences…
- 29 March 1994
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.
"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.
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
Codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome.
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.