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Measures of Codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms

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dc.contributor.authorFriberg, Markus
dc.contributor.authorGonnet, Pedro
dc.contributor.authorBarral, Yves
dc.contributor.authorSchraudolph, Nicol
dc.contributor.authorGonnet, Gaston H
dc.coverage.spatialZurich Switzerland
dc.date.accessioned2015-12-07T22:33:45Z
dc.date.createdSeptermber 11-13 2006
dc.date.issued2006
dc.date.updated2015-12-07T10:35:19Z
dc.description.abstractProtein translation is a rapid and accurate process, which has been optimized by evolution. Recently, it has been shown that tRNA reusage influences translation speed. We present the tRNA Pairing Index (TPI), a novel index to measure the degree of tRNA reusage in any gene. We describe two variants of the index, how to combine various such indices to a single one and an efficient algorithm for their computation. A statistical analysis of gene expression groups indicate that cell cycle genes have high TPI. This result is independent of other biases like GC content and codon bias. Furthermore, we find an additional unexpected codon bias that seems related to a context sensitive DNA repair.
dc.identifier.isbn3540395830
dc.identifier.urihttp://hdl.handle.net/1885/23407
dc.publisherSpringer
dc.relation.ispartofseriesInternational Workshop on Algorithms in Bioinformatics (WABI 2006)
dc.sourceProoceedings of the 6th International Workshop on Algorithms in Bioinformatics (WABI 2006)
dc.subjectKeywords: Computation theory; DNA; Proteins; RNA; Yeast; DNA repair mechanisms; Evolution; Protein translation; tRNA Pairing Index (TPI); Biomedical engineering
dc.titleMeasures of Codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms
dc.typeConference paper
local.bibliographicCitation.lastpage11
local.bibliographicCitation.startpage1
local.contributor.affiliationFriberg, Markus, Swiss Federal Institute of Technology (ETH)
local.contributor.affiliationGonnet, Pedro, Swiss Federal Institute of Technology (ETH)
local.contributor.affiliationBarral, Yves, Swiss Federal Institute of Technology (ETH)
local.contributor.affiliationSchraudolph, Nicol, College of Engineering and Computer Science, ANU
local.contributor.affiliationGonnet, Gaston H, Swiss Federal Institute of Technology (ETH)
local.contributor.authoruidSchraudolph, Nicol, a205905
local.description.embargo2037-12-31
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.absfor080109 - Pattern Recognition and Data Mining
local.identifier.ariespublicationu8803936xPUB26
local.identifier.scopusID2-s2.0-33750258647
local.type.statusPublished Version

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