Open AccessDragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants
Author(s) -
Arturo Magana-Mora,
Haitham Ashoor,
Boris R. Janković,
Allan Kamau,
Karim Awara,
Rajesh Chowdhary,
John A. C. Archer,
Vladimir B. Bajić
Publication year - 2012
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/bts638
Subject(s) - arabidopsis , annotation , arabidopsis thaliana , computational biology , genome , source code , translation (biology) , biology , eukaryotic translation , populus trichocarpa , identification (biology) , computer science , genetics , messenger rna , gene , botany , programming language , mutant
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.
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