Seforta, an integrated tool for detecting the signature of selection in coding sequences

BMC Research Notes

Andrea Porceddu¹  Giampiera Milia¹  Sara Melito¹  Salvatore Camiolo¹ 

[1] Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy

关键词: Translational accuracy;    Translation optimization;    Codon bias;   

Others  :  1133735
DOI  :  10.1186/1756-0500-7-240

 received in 2014-01-09, accepted in 2014-04-11,  发布年份 2014

【 摘 要 】

Background

The 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.

Findings

We 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.

Conclusions

Seforta 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.

【 授权许可】

   
2014 Camiolo et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Kramer EB, Farabaugh PJ: The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 2007, 13:87-96.
• [2]Pakula AA, Sauer RT: Genetic analysis of protein stability and function. Annu Rev Genet 1989, 23:289-310.
• [3]Akashi H: Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 1994, 136:927-935.
• [4]Drummond DA, Wilke CO: The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 2009, 10:715-724.
• [5]Precup J, Parker J: Missense misreading of asparagine codons as a function of codon identity and context. J Biol Chem 1987, 262:11351-11355.
• [6]Akashi H: Translational selection and yeast proteome evolution. Genetics 2003, 164:1291-1303.
• [7]Mantel N, Haenszel W: Statistical aspects of the analysis of data from retrospective analysis of disease. JNCI 1959, 22:719.
• [8]Hershberg R, Petrov DA: Selection on codon bias. Annu Rev Genet 2008, 42:287-299.
• [9]Hershberg R, Petrov DA: General rules for optimal codon choice. PLoS Genet 2009, 5:e1000556.
• [10]Novembre JA: Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol 2002, 19:1390-1394.
• [11]Drummond DA, Wilke CO: Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134:341-352.