The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Paul M. Sharp,Wen-Hsiung Li +1 more
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TLDR
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.Abstract:Â
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.read more
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The Complete Genome Sequence of Escherichia coli K-12
Frederick R. Blattner,Guy Plunkett,Craig A. Bloch,Nicole T. Perna,Valerie Burland,Monica Riley,Julio Collado-Vides,Jeremy D. Glasner,Christopher K. Rode,George F. Mayhew,Jason Gregor,Nelson Wayne Davis,Heather A. Kirkpatrick,Michael A. Goeden,Debra J. Rose,Bob Mau,Ying Shao +16 more
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
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Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
TL;DR: MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date, identifying 131 proteins with three or more predicted transmembrane domains which allowed us to map the soluble domains of many of the integral membrane proteins.
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Global analysis of protein expression in yeast
Sina Ghaemmaghami,Won-Ki Huh,Kiowa Bower,Russell W. Howson,Archana Belle,Noah Dephoure,Erin K. O'Shea,Jonathan S. Weissman +7 more
TL;DR: A Saccharomyces cerevisiae fusion library is created where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location, and it is found that about 80% of the proteome is expressed during normal growth conditions.
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Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Markus Hafner,Markus Landthaler,Lukas Burger,Mohsen Khorshid,Jean Hausser,Philipp Berninger,Andrea Rothballer,Manuel Ascano,Anna-Carina Jungkamp,Mathias Munschauer,Alexander Ulrich,Greg S. Wardle,Scott Dewell,Mihaela Zavolan,Thomas Tuschl +14 more
TL;DR: This study developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs and revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions.
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A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity
Chava Kimchi-Sarfaty,Jung Mi Oh,In-Wha Kim,Zuben E. Sauna,Anna Maria Calcagno,Suresh V. Ambudkar,Michael M. Gottesman +6 more
TL;DR: It is hypothesized that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.
References
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Book
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TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Journal ArticleDOI
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Journal ArticleDOI
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Manolo Gouy,Christian Gautier +1 more
TL;DR: Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration.
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