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

Markus T. Friberg; Pedro Gonnet; Yves Barral; Nicol N. Schraudolph; Gaston H. Gonnet

doi:10.1007/11851561_1

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

Markus T. Friberg^*, Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Gaston H. Gonnet

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

8 Citations (Scopus)

Abstract

Protein 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.

Original language	English
Title of host publication	Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
Publisher	Springer Verlag
Pages	1-11
Number of pages	11
ISBN (Print)	3540395830, 9783540395836
DOIs	https://doi.org/10.1007/11851561_1
Publication status	Published - 2006
Event	6th International Workshop on Algorithms in Bioinformatics, WABI 2006 - Zurich, Switzerland Duration: 11 Sept 2006 → 13 Sept 2006

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4175 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	6th International Workshop on Algorithms in Bioinformatics, WABI 2006
Country/Territory	Switzerland
City	Zurich
Period	11/09/06 → 13/09/06

Access to Document

10.1007/11851561_1

Cite this

Friberg, M. T., Gonnet, P., Barral, Y., Schraudolph, N. N., & Gonnet, G. H. (2006). Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms. In Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings (pp. 1-11). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4175 LNBI). Springer Verlag. https://doi.org/10.1007/11851561_1

Friberg, Markus T. ; Gonnet, Pedro ; Barral, Yves et al. / Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms. Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer Verlag, 2006. pp. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{6ba9a8a880d24b53989ca98924affc2b,

title = "Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms",

abstract = "Protein 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.",

author = "Friberg, {Markus T.} and Pedro Gonnet and Yves Barral and Schraudolph, {Nicol N.} and Gonnet, {Gaston H.}",

year = "2006",

doi = "10.1007/11851561_1",

language = "English",

isbn = "3540395830",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "1--11",

booktitle = "Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings",

address = "Germany",

note = "6th International Workshop on Algorithms in Bioinformatics, WABI 2006 ; Conference date: 11-09-2006 Through 13-09-2006",

}

Friberg, MT, Gonnet, P, Barral, Y, Schraudolph, NN & Gonnet, GH 2006, Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms. in Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4175 LNBI, Springer Verlag, pp. 1-11, 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, Zurich, Switzerland, 11/09/06. https://doi.org/10.1007/11851561_1

Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms. / Friberg, Markus T.; Gonnet, Pedro; Barral, Yves et al.
Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer Verlag, 2006. p. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4175 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms

AU - Friberg, Markus T.

AU - Gonnet, Pedro

AU - Barral, Yves

AU - Schraudolph, Nicol N.

AU - Gonnet, Gaston H.

PY - 2006

Y1 - 2006

N2 - Protein 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.

AB - Protein 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.

UR - http://www.scopus.com/inward/record.url?scp=33750258647&partnerID=8YFLogxK

U2 - 10.1007/11851561_1

DO - 10.1007/11851561_1

M3 - Conference contribution

SN - 3540395830

SN - 9783540395836

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 1

EP - 11

BT - Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings

PB - Springer Verlag

T2 - 6th International Workshop on Algorithms in Bioinformatics, WABI 2006

Y2 - 11 September 2006 through 13 September 2006

ER -

Friberg MT, Gonnet P, Barral Y, Schraudolph NN, Gonnet GH. Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms. In Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings. Springer Verlag. 2006. p. 1-11. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/11851561_1

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

Abstract

Publication series

Conference

Access to Document

Other files and links

Fingerprint

Cite this