Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants

• Published in: Bioinformatics Vol. 29; no. 1; pp. 117 - 118
• Main Authors: Magana-Mora, Arturo, Ashoor, Haitham, Jankovic, Boris R, Kamau, Allan, Awara, Karim, Chowdhary, Rajesh, Archer, John A C, Bajic, Vladimir B
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2013
• Subjects: Applications Note; Arabidopsis - genetics; Arabidopsis thaliana; Genome, Plant; Genomics; Internet; Neural Networks (Computer); Nucleotide Motifs; Peptide Chain Initiation, Translational; Populus trichocarpa; Sensitivity and Specificity; Sequence Analysis, DNA; Software; Vitis vinifera
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts638

In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation. Our tool is implemented as an artificial neural network. It is available as a web-based tool and, together with the source code, the list of features, and data used for model development, is accessible at http://cbrc.kaust.edu.sa/dts.