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

Bioinformatics. 2013 Jan 1;29(1):117-8. doi: 10.1093/bioinformatics/bts638. Epub 2012 Oct 30.


Summary: 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.

Availability and implementation: 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.

MeSH terms

  • Arabidopsis / genetics*
  • Genome, Plant
  • Genomics
  • Internet
  • Neural Networks, Computer
  • Nucleotide Motifs
  • Peptide Chain Initiation, Translational*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Software*