A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
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* Corresponding author: Laura F Landweber lfl@princeton.edu
Genome Biology 2001, 2:research0010-research0010.13 doi:10.1186/gb-2001-2-4-research0010
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Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species Makedonka Mitreva, Michael C Wendl, John Martin, Todd Wylie, Yong Yin, Allan Larson, John Parkinson, Robert H Waterston, James P McCarter Genome Biology 2006, 7:R75 (14 August 2006) A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage. |
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Genomic and proteomic adaptations to growth at high temperature Donal A Hickey, Gregory AC Singer Genome Biology 2004, 5:117 (30 September 2004) The evidence is discussed for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes. |
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The relationship of protein conservation and sequence length David J Lipman, Alexander Souvorov, Eugene V Koonin, Anna R Panchenko, Tatiana A Tatusova BMC Evolutionary Biology 2002, 2:20 (1 November 2002) Proteins conserved across kingdoms are likely to be longer than more divergent proteins, suggesting evolutionary trends in favour of shortness.
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Deposited research article
Preferred codons and amino acid couples in hyperthermophiles Sávio de Farias, Maria Bonato Genome Biology 2002, 3:preprint0006-preprint0006.18 (19 July 2002) The preferential usage of certain couples of amino acids and codons in thermal adaptation was investigated, by comparative proteome analysis, using 28 complete genomes. The results suggested that the Glu+Lys/Gln+His ratio may provide a useful mark for distinguishing hyperthermophilic, thermophilic and mesophilic prokaryotes |
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On the species of origin: diagnosing the source of symbiotic transcripts Peter T Hraber, Jennifer W Weller Genome Biology 2001, 2:research0037-research0037.14 (23 August 2001) Symbiotic interactions range from pathogenic to mutualistic, and many of the underlying molecular mechanisms remain to be discovered. Given a sequence expressed in an interaction between two symbionts, the challenge is to determine from which organism the transcript originated. Previous investigations into GC content and comparative similarity searching provide solutions, but a comparative lexical analysis, which uses a likelihood-ratio test of hexamer counts, is more powerful. Microbial transcripts comprised 75% of a |