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BMC Research Notes

, 7:240

First Online: 16 April 2014Received: 09 January 2014Accepted: 11 April 2014DOI: 10.1186-1756-0500-7-240

Cite this article as: Camiolo, S., Melito, S., Milia, G. et al. BMC Res Notes 2014 7: 240. doi:10.1186-1756-0500-7-240

Abstract

BackgroundThe majority of amino acid residues are encoded by more than one codon, and a bias in the usage of such synonymous codons has been repeatedly demonstrated. One assumption is that this phenomenon has evolved to improve the efficiency of translation by reducing the time required for the recruitment of isoacceptors. The most abundant tRNA species are preferred at sites on the protein which are key for its functionality, a behavior which has been termed -translational accuracy-. Although observed in many species, as yet no public domain software has been made available for its quantification.

FindingsWe present here Seforta Selection for Translational Accuracy, a program designed to quantify translational accuracy. It searches for synonymous codon usage bias in both conserved and non-conserved regions of coding sequences and computes a cumulative odds ratio and a Z-score. The specification of a set of preferred codons is desirable, but the program can also generate these. Finally, a randomization protocol calculates the probability that preferred codon combinations could have arisen by chance.

ConclusionsSeforta is the first public domain program able to quantify translational accuracy. It comes with a simple graphical user interface and can be readily installed and adjusted to the user-s requirements.

KeywordsCodon bias Translation optimization Translational accuracy Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-7-240 contains supplementary material, which is available to authorized users.

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Autor: Salvatore Camiolo - Sara Melito - Giampiera Milia - Andrea Porceddu

Fuente: https://link.springer.com/







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