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Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large and computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the numberof nucleotide substitutions per site is very large. Expand
The Transcriptional Landscape of the Mammalian Genome
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. Expand
Codon usage tabulated from international DNA sequence databases: status for the year 2000
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used byExpand
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
  • H. Akashi, T. Gojobori
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences…
  • 19 March 2002
Evidence is provided that amino acid composition in the proteomes of E. coli and Bacillus subtilis reflects the action of natural selection to enhance metabolic efficiency and increases in the abundance of less energetically costly amino acids in highly expressed proteins are shown. Expand
A method for detecting positive selection at single amino acid sites.
Computer simulation showed that this method accurately estimated the numbers of synonymous and nonsynonymous substitutions per site, as long as the substitution number on each branch was relatively small, and the false-positive rate for detecting the selective force was generally low. Expand
Biased biological functions of horizontally transferred genes in prokaryotic genomes
It is quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions, so the transferability of genes seems to depend heavily on their functions. Expand
The dynamic genome of Hydra
Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction. Expand
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics. Expand
Molecular cloning and expression of a member of the aquaporin family with permeability to glycerol and urea in addition to water expressed at the basolateral membrane of kidney collecting duct cells.
Although to a smaller degree, AQP3 also facilitated the transport of nonionic small solutes such as urea and glycerol, while the previously cloned water channels are permeable only to water when expressed in Xenopus oocytes. Expand
Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses.
The clustering based on the capsid N/S domain successfully distinguished the NLV as well as the groupingbased on the antigenicity, as determined by both antigen and antibody ELISAs with recombinant virus-like particles. Expand