title: Seforta, an integrated tool for detecting the signature of selection in coding sequences.
abstract: 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.
  
  
  RESULTS
  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.
authors.affiliation: Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy. s.camiolo@uniss.it.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Camiolo
authors.forename: Sara
authors.initials: S
authors.lastname: Melito
authors.forename: Giampiera
authors.initials: G
authors.lastname: Milia
authors.forename: Andrea
authors.initials: A
authors.lastname: Porceddu
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D012641:Selection, Genetic; D012984:Software
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