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

Handle URI:
http://hdl.handle.net/10754/325435
Title:
Dragon TIS Spotter: An Arabidopsis-derived predictor of translation initiation sites in plants
Authors:
Magana-Mora, Arturo ( 0000-0001-8696-7068 ) ; Ashoor, Haitham ( 0000-0003-2527-0317 ) ; Jankovic, Boris R.; Kamau, Allan; Awara, Karim; Chowdhary, Rajesh; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
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.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Magana-Mora A, Ashoor H, Jankovic BR, Kamau A, Awara K, et al. (2012) Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics 29: 117-118. doi:10.1093/bioinformatics/bts638.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
Issue Date:
30-Oct-2012
DOI:
10.1093/bioinformatics/bts638
PubMed ID:
23110968
PubMed Central ID:
PMC3530916
Type:
Article
ISSN:
13674803
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorMagana-Mora, Arturoen
dc.contributor.authorAshoor, Haithamen
dc.contributor.authorJankovic, Boris R.en
dc.contributor.authorKamau, Allanen
dc.contributor.authorAwara, Karimen
dc.contributor.authorChowdhary, Rajeshen
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2014-08-27T09:51:13Z-
dc.date.available2014-08-27T09:51:13Z-
dc.date.issued2012-10-30en
dc.identifier.citationMagana-Mora A, Ashoor H, Jankovic BR, Kamau A, Awara K, et al. (2012) Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics 29: 117-118. doi:10.1093/bioinformatics/bts638.en
dc.identifier.issn13674803en
dc.identifier.pmid23110968en
dc.identifier.doi10.1093/bioinformatics/bts638en
dc.identifier.urihttp://hdl.handle.net/10754/325435en
dc.description.abstractIn 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.en
dc.language.isoenen
dc.publisherOxford University Press (OUP)en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0en
dc.subjectArabidopsisen
dc.subjectArabidopsis thalianaen
dc.subjectEukaryotaen
dc.subjectPopulus trichocarpaen
dc.subjectVitaceaeen
dc.subjectVitis viniferaen
dc.subjectArabidopsisen
dc.subjectartificial neural networken
dc.subjectcomputer programen
dc.subjectDNA sequenceen
dc.subjectgeneticsen
dc.subjectgenomicsen
dc.subjectInterneten
dc.subjectnucleotide motifen
dc.subjectplant genomeen
dc.subjectRNA translationen
dc.subjectsensitivity and specificityen
dc.subjectArabidopsisen
dc.subjectGenome, Planten
dc.subjectGenomicsen
dc.subjectInterneten
dc.subjectNeural Networks (Computer)en
dc.subjectNucleotide Motifsen
dc.subjectPeptide Chain Initiation, Translationalen
dc.subjectSensitivity and Specificityen
dc.subjectSequence Analysis, DNAen
dc.subjectSoftwareen
dc.titleDragon TIS Spotter: An Arabidopsis-derived predictor of translation initiation sites in plantsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC3530916en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionBiomedical Formatics Research Center, MCRF, Marshfield Clinic, Marshfield, WI 54449, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorAshoor, Haithamen
kaust.authorArcher, John A.C.en
kaust.authorBajic, Vladimir B.en
kaust.authorMagana-Mora, Arturoen
kaust.authorJankovic, Boris R.en
kaust.authorKamau, Allanen
kaust.authorAwara, Karimen

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