k-mer sparse matrix model for genetic sequence and its applications in sequence comparison.
Identifieur interne : 001A11 ( Main/Exploration ); précédent : 001A10; suivant : 001A12k-mer sparse matrix model for genetic sequence and its applications in sequence comparison.
Auteurs : Jia Wen [République populaire de Chine] ; Yuyan Zhang [République populaire de Chine] ; Stephen S T. Yau [République populaire de Chine]Source :
- Journal of theoretical biology [ 1095-8541 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Base Sequence.
- methods : Computational Biology, Sequence Analysis.
- Models, Genetic.
Abstract
Based on the k-mer model for genetic sequence, a k-mer sparse matrix representation is proposed to denote the types and sites of k-mers appearing in a genetic sequence, and there exists a one-to-one relationship between a genetic sequence and its associated k-mer sparse matrix. With the singular value decomposition of the k-mer sparse matrix, the k-mer singular value vector is constructed and utilized to numerically quantify the characteristics of a genetic sequence. We investigate and evaluate the optimum value k(⁎) chosen for our k-mer sparse matrix model for genetic sequence. To show the usefulness of our k-mer sparse matrix model method, it is applied to the comparison of genetic sequences, and the results obtained fully demonstrate that our proposed method is very powerful in analyzing and determining the relationships of genetic sequences.
DOI: 10.1016/j.jtbi.2014.08.028
PubMed: 25158165
Affiliations:
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Electronic address: wenjia198021@126.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Information Engineering, Suihua University, Suihua 152061</wicri:regionArea><wicri:noRegion>Suihua 152061</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Yuyan" sort="Zhang, Yuyan" uniqKey="Zhang Y" first="Yuyan" last="Zhang">Yuyan Zhang</name><affiliation wicri:level="1"><nlm:affiliation>School of Agriculture and Hydraulic Engineering, Suihua University, Suihua 152061, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Agriculture and Hydraulic Engineering, Suihua University, Suihua 152061</wicri:regionArea><wicri:noRegion>Suihua 152061</wicri:noRegion></affiliation></author><author><name sortKey="Yau, Stephen S T" sort="Yau, Stephen S T" uniqKey="Yau S" first="Stephen S T" last="Yau">Stephen S T. Yau</name><affiliation wicri:level="1"><nlm:affiliation>Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China. Electronic address: yau@uic.edu.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Mathematical Sciences, Tsinghua University, Beijing 100084</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Journal of theoretical biology</title><idno type="eISSN">1095-8541</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (genetics)</term><term>Computational Biology (methods)</term><term>Models, Genetic</term><term>Sequence Analysis (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence ()</term><term>Biologie informatique ()</term><term>Modèles génétiques</term><term>Séquence nucléotidique (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Sequence</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Models, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence</term><term>Biologie informatique</term><term>Modèles génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Based on the k-mer model for genetic sequence, a k-mer sparse matrix representation is proposed to denote the types and sites of k-mers appearing in a genetic sequence, and there exists a one-to-one relationship between a genetic sequence and its associated k-mer sparse matrix. With the singular value decomposition of the k-mer sparse matrix, the k-mer singular value vector is constructed and utilized to numerically quantify the characteristics of a genetic sequence. We investigate and evaluate the optimum value k(⁎) chosen for our k-mer sparse matrix model for genetic sequence. To show the usefulness of our k-mer sparse matrix model method, it is applied to the comparison of genetic sequences, and the results obtained fully demonstrate that our proposed method is very powerful in analyzing and determining the relationships of genetic sequences. </div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wen, Jia" sort="Wen, Jia" uniqKey="Wen J" first="Jia" last="Wen">Jia Wen</name></noRegion><name sortKey="Yau, Stephen S T" sort="Yau, Stephen S T" uniqKey="Yau S" first="Stephen S T" last="Yau">Stephen S T. Yau</name><name sortKey="Zhang, Yuyan" sort="Zhang, Yuyan" uniqKey="Zhang Y" first="Yuyan" last="Zhang">Yuyan Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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