Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.
Identifieur interne : 002728 ( Main/Exploration ); précédent : 002727; suivant : 002729Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.
Auteurs : Arturo Magana-Mora [Arabie saoudite] ; Haitham Ashoor ; Boris R. Jankovic ; Allan Kamau ; Karim Awara ; Rajesh Chowdhary ; John A C. Archer ; Vladimir B. BajicSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2013.
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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.
DOI: 10.1093/bioinformatics/bts638
PubMed: 23110968
PubMed Central: PMC3530916
Affiliations:
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Le document en format XML
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Jankovic</name></author><author><name sortKey="Kamau, Allan" sort="Kamau, Allan" uniqKey="Kamau A" first="Allan" last="Kamau">Allan Kamau</name></author><author><name sortKey="Awara, Karim" sort="Awara, Karim" uniqKey="Awara K" first="Karim" last="Awara">Karim Awara</name></author><author><name sortKey="Chowdhary, Rajesh" sort="Chowdhary, Rajesh" uniqKey="Chowdhary R" first="Rajesh" last="Chowdhary">Rajesh Chowdhary</name></author><author><name sortKey="Archer, John A C" sort="Archer, John A C" uniqKey="Archer J" first="John A C" last="Archer">John A C. Archer</name></author><author><name sortKey="Bajic, Vladimir B" sort="Bajic, Vladimir B" uniqKey="Bajic V" first="Vladimir B" last="Bajic">Vladimir B. 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Jankovic</name></author><author><name sortKey="Kamau, Allan" sort="Kamau, Allan" uniqKey="Kamau A" first="Allan" last="Kamau">Allan Kamau</name></author><author><name sortKey="Awara, Karim" sort="Awara, Karim" uniqKey="Awara K" first="Karim" last="Awara">Karim Awara</name></author><author><name sortKey="Chowdhary, Rajesh" sort="Chowdhary, Rajesh" uniqKey="Chowdhary R" first="Rajesh" last="Chowdhary">Rajesh Chowdhary</name></author><author><name sortKey="Archer, John A C" sort="Archer, John A C" uniqKey="Archer J" first="John A C" last="Archer">John A C. Archer</name></author><author><name sortKey="Bajic, Vladimir B" sort="Bajic, Vladimir B" uniqKey="Bajic V" first="Vladimir B" last="Bajic">Vladimir B. Bajic</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Genome, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Internet (MeSH)</term><term>Neural Networks, Computer (MeSH)</term><term>Nucleotide Motifs (MeSH)</term><term>Peptide Chain Initiation, Translational (MeSH)</term><term>Sensitivity and Specificity (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Arabidopsis (génétique)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Initiation de la traduction (MeSH)</term><term>Internet (MeSH)</term><term>Logiciel (MeSH)</term><term>Motifs nucléotidiques (MeSH)</term><term>Sensibilité et spécificité (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Genomics</term><term>Internet</term><term>Neural Networks, Computer</term><term>Nucleotide Motifs</term><term>Peptide Chain Initiation, Translational</term><term>Sensitivity and Specificity</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génome végétal</term><term>Génomique</term><term>Initiation de la traduction</term><term>Internet</term><term>Logiciel</term><term>Motifs nucléotidiques</term><term>Sensibilité et spécificité</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>SUMMARY</b></p><p>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.</p></div><div type="abstract" xml:lang="en"><p><b>AVAILABILITY AND IMPLEMENTATION</b></p><p>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.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">23110968</PMID><DateCompleted><Year>2013</Year><Month>07</Month><Day>29</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>29</Volume><Issue>1</Issue><PubDate><Year>2013</Year><Month>Jan</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.</ArticleTitle><Pagination><MedlinePgn>117-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bts638</ELocationID><Abstract><AbstractText Label="SUMMARY" NlmCategory="CONCLUSIONS">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.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">Our tool is implemented as an artificial neural network. 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IdType="pubmed">7880905</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Arabie saoudite</li></country></list><tree><noCountry><name sortKey="Archer, John A C" sort="Archer, John A C" uniqKey="Archer J" first="John A C" last="Archer">John A C. Archer</name><name sortKey="Ashoor, Haitham" sort="Ashoor, Haitham" uniqKey="Ashoor H" first="Haitham" last="Ashoor">Haitham Ashoor</name><name sortKey="Awara, Karim" sort="Awara, Karim" uniqKey="Awara K" first="Karim" last="Awara">Karim Awara</name><name sortKey="Bajic, Vladimir B" sort="Bajic, Vladimir B" uniqKey="Bajic V" first="Vladimir B" last="Bajic">Vladimir B. Bajic</name><name sortKey="Chowdhary, Rajesh" sort="Chowdhary, Rajesh" uniqKey="Chowdhary R" first="Rajesh" last="Chowdhary">Rajesh Chowdhary</name><name sortKey="Jankovic, Boris R" sort="Jankovic, Boris R" uniqKey="Jankovic B" first="Boris R" last="Jankovic">Boris R. Jankovic</name><name sortKey="Kamau, Allan" sort="Kamau, Allan" uniqKey="Kamau A" first="Allan" last="Kamau">Allan Kamau</name></noCountry><country name="Arabie saoudite"><noRegion><name sortKey="Magana Mora, Arturo" sort="Magana Mora, Arturo" uniqKey="Magana Mora A" first="Arturo" last="Magana-Mora">Arturo Magana-Mora</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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