Feature-Based and String-Based Models for Predicting RNA-Protein Interaction.
Identifieur interne : 000969 ( Main/Exploration ); précédent : 000968; suivant : 000970Feature-Based and String-Based Models for Predicting RNA-Protein Interaction.
Auteurs : Donald Adjeroh [États-Unis] ; Maen Allaga [États-Unis] ; Jun Tan [États-Unis] ; Jie Lin [République populaire de Chine] ; Yue Jiang [République populaire de Chine] ; Ahmed Abbasi [États-Unis] ; Xiaobo Zhou [États-Unis]Source :
- Molecules (Basel, Switzerland) [ 1420-3049 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA, RNA-Binding Proteins.
- chemical , metabolism : RNA, RNA, Long Noncoding, RNA-Binding Proteins.
- Algorithms, Databases, Protein, Models, Molecular, Nucleic Acid Conformation.
Abstract
In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI). In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences), and structure information (protein and RNA secondary structures). This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.
DOI: 10.3390/molecules23030697
PubMed: 29562711
Affiliations:
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26508</wicri:regionArea><placeName><region type="state">Virginie-Occidentale</region></placeName></affiliation></author><author><name sortKey="Allaga, Maen" sort="Allaga, Maen" uniqKey="Allaga M" first="Maen" last="Allaga">Maen Allaga</name><affiliation wicri:level="2"><nlm:affiliation>Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26508, USA. maenallaga@gmail.com.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26508</wicri:regionArea><placeName><region type="state">Virginie-Occidentale</region></placeName></affiliation></author><author><name sortKey="Tan, Jun" sort="Tan, Jun" uniqKey="Tan J" first="Jun" last="Tan">Jun Tan</name><affiliation wicri:level="2"><nlm:affiliation>Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26508, USA. jforce716@gmail.com.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26508</wicri:regionArea><placeName><region type="state">Virginie-Occidentale</region></placeName></affiliation></author><author><name sortKey="Lin, Jie" sort="Lin, Jie" uniqKey="Lin J" first="Jie" last="Lin">Jie Lin</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Software, Fujian Normal University, Fuzhou 350108, China. linjie891@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Faculty of Software, Fujian Normal University, Fuzhou 350108</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author><author><name sortKey="Jiang, Yue" sort="Jiang, Yue" uniqKey="Jiang Y" first="Yue" last="Jiang">Yue Jiang</name><affiliation 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Xiaobo" sort="Zhou, Xiaobo" uniqKey="Zhou X" first="Xiaobo" last="Zhou">Xiaobo Zhou</name><affiliation wicri:level="2"><nlm:affiliation>McGovern Medical School, and School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA. Xiaobo.Zhou@uth.tmc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>McGovern Medical School, and School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author></analytic><series><title level="j">Molecules (Basel, Switzerland)</title><idno type="eISSN">1420-3049</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Databases, Protein</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>RNA (chemistry)</term><term>RNA (metabolism)</term><term>RNA, Long Noncoding (metabolism)</term><term>RNA-Binding Proteins (chemistry)</term><term>RNA-Binding Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ()</term><term>ARN (métabolisme)</term><term>ARN long non codant (métabolisme)</term><term>Algorithmes</term><term>Bases de données de protéines</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Protéines de liaison à l'ARN ()</term><term>Protéines de liaison à l'ARN (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA</term><term>RNA, Long Noncoding</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN</term><term>ARN long non codant</term><term>Protéines de liaison à l'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Protein</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN</term><term>Algorithmes</term><term>Bases de données de protéines</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Protéines de liaison à l'ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI). In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences), and structure information (protein and RNA secondary structures). This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Fujian</li><li>Texas</li><li>Virginie</li><li>Virginie-Occidentale</li></region><settlement><li>Fuzhou</li></settlement></list><tree><country name="États-Unis"><region name="Virginie-Occidentale"><name sortKey="Adjeroh, Donald" sort="Adjeroh, Donald" uniqKey="Adjeroh D" first="Donald" last="Adjeroh">Donald Adjeroh</name></region><name sortKey="Abbasi, Ahmed" sort="Abbasi, Ahmed" uniqKey="Abbasi A" first="Ahmed" last="Abbasi">Ahmed Abbasi</name><name sortKey="Allaga, Maen" sort="Allaga, Maen" uniqKey="Allaga M" first="Maen" last="Allaga">Maen Allaga</name><name sortKey="Tan, Jun" sort="Tan, Jun" uniqKey="Tan J" first="Jun" last="Tan">Jun Tan</name><name sortKey="Zhou, Xiaobo" sort="Zhou, Xiaobo" uniqKey="Zhou X" first="Xiaobo" last="Zhou">Xiaobo Zhou</name></country><country name="République populaire de Chine"><region name="Fujian"><name sortKey="Lin, Jie" sort="Lin, Jie" uniqKey="Lin J" first="Jie" last="Lin">Jie Lin</name></region><name sortKey="Jiang, Yue" sort="Jiang, Yue" uniqKey="Jiang Y" first="Yue" last="Jiang">Yue Jiang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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