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

Camiolo, Salvatore and Melito, Sara and Milia, Giampiera and Porceddu, Andrea (2014) Seforta, an integrated tool for detecting the signature of selection in coding sequences. BMC Research Notes, Vol. 7 (240), p. 3. ISSN 1756-0500. Article.

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DOI: 10.1186/1756-0500-7-240


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.

Item Type:Article
ID Code:10245
Uncontrolled Keywords:Codon bias, translation optimization, translational accuracy
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/07 Genetica agraria
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Agraria
Publisher:BioMed Central
Copyright Holders:© 2014 Camiolo et al.
Deposited On:31 Oct 2014 08:20

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