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

Arturo Magana-Mora; Haitham Ashoor; Boris R. Jankovic; Allan Kamau; Karim Awara; Rajesh Chowdhary; John A.C. Archer; Vladimir B. Bajic

doi:10.1093/bioinformatics/bts638

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

Arturo Magana-Mora, Haitham Ashoor, Boris R. Jankovic, Allan Kamau, Karim Awara, Rajesh Chowdhary, John A.C. Archer, Vladimir B. Bajic

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

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. The Author(s) 2012. Published by Oxford University Press.

Original language	English (US)
Pages (from-to)	117-118
Number of pages	2
Journal	Bioinformatics
Volume	29
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/bts638
State	Published - Oct 30 2012

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01

ASJC Scopus subject areas

Biochemistry
Computational Theory and Mathematics
Computational Mathematics
Molecular Biology
Statistics and Probability
Computer Science Applications

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10.1093/bioinformatics/bts638

https://repository.kaust.edu.sa/bitstream/10754/325435/1/Article-Bioinforma-Dragon_TIS-2013.pdf

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title = "Dragon TIS Spotter: An Arabidopsis-derived predictor of translation initiation sites in plants",

abstract = "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. The Author(s) 2012. Published by Oxford University Press.",

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AU - Magana-Mora, Arturo

AU - Ashoor, Haitham

AU - Jankovic, Boris R.

AU - Kamau, Allan

AU - Awara, Karim

AU - Chowdhary, Rajesh

AU - Archer, John A.C.

AU - Bajic, Vladimir B.

N1 - KAUST Repository Item: Exported on 2020-10-01

PY - 2012/10/30

Y1 - 2012/10/30

N2 - 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. The Author(s) 2012. Published by Oxford University Press.

AB - 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. The Author(s) 2012. Published by Oxford University Press.

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

Abstract

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ASJC Scopus subject areas

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