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

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

Author information

1
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia.

Abstract

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.

PMID:
23110968
PMCID:
PMC3530916
DOI:
10.1093/bioinformatics/bts638
[Indexed for MEDLINE]
Free PMC Article

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