Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
Identifieur interne : 001778 ( Main/Exploration ); précédent : 001777; suivant : 001779Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
Auteurs : Yinglei Song [États-Unis] ; Chunmei Liu [États-Unis] ; Xiuzhen Huang [États-Unis] ; Russell L. Malmberg [États-Unis] ; Ying Xu [États-Unis] ; Liming Cai [États-Unis]Source :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity but also spatially conserved conformations caused by residue interactions, and consequently is computationally intractable. It is difficult to cope with the inefficiency without compromising alignment accuracy, especially for structure search in genomes or large databases. This paper introduces a novel method and a parameterized algorithm for structure-sequence alignment. Both the structure and the sequence are represented as graphs, where in general the graph for a biopolymer structure has a naturally small tree width. The algorithm constructs an optimal alignment by finding in the sequence graph the maximum valued subgraph isomorphic to the structure graph. It has the computational time complexity O(k t N 2) for the structure of N residues and its tree decomposition of width t. The parameter k, small in nature, is determined by a statistical cutoff for the correspondence between the structure and the sequence. The paper demonstrates a successful application of the algorithm to developing a fast program for RNA structural homology search.
Url:
DOI: 10.1007/11557067_31
Affiliations:
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Malmberg</name></author><author><name sortKey="Xu, Ying" sort="Xu, Ying" uniqKey="Xu Y" first="Ying" last="Xu">Ying Xu</name></author><author><name sortKey="Cai, Liming" sort="Cai, Liming" uniqKey="Cai L" first="Liming" last="Cai">Liming Cai</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:F6316235B91C7ECC5DF547655E0F3533F36E03B0</idno><date when="2005" year="2005">2005</date><idno type="doi">10.1007/11557067_31</idno><idno type="url">https://api.istex.fr/ark:/67375/HCB-KDXGGF10-K/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000156</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000156</idno><idno type="wicri:Area/Istex/Curation">000124</idno><idno type="wicri:Area/Istex/Checkpoint">000263</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000263</idno><idno type="wicri:doubleKey">0302-9743:2005:Song Y:efficient:parameterized:algorithm</idno><idno type="wicri:Area/Main/Merge">001788</idno><idno type="wicri:Area/Main/Curation">001778</idno><idno type="wicri:Area/Main/Exploration">001778</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment</title><author><name sortKey="Song, Yinglei" sort="Song, Yinglei" uniqKey="Song Y" first="Yinglei" last="Song">Yinglei Song</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Computer Science, Univ. of Georgia, 30602, Athens, GA</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author><author><name sortKey="Liu, Chunmei" sort="Liu, Chunmei" uniqKey="Liu C" first="Chunmei" last="Liu">Chunmei Liu</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Computer Science, Univ. of Georgia, 30602, Athens, GA</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Huang, Xiuzhen" sort="Huang, Xiuzhen" uniqKey="Huang X" first="Xiuzhen" last="Huang">Xiuzhen Huang</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Computer Science, Arkansas State Univ., State University, 72467, AR</wicri:regionArea><placeName><region type="state">Arkansas</region></placeName></affiliation></author><author><name sortKey="Malmberg, Russell L" sort="Malmberg, Russell L" uniqKey="Malmberg R" first="Russell L." last="Malmberg">Russell L. Malmberg</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Plant Biology, Univ. of Georgia, 30602, Athens, GA</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Xu, Ying" sort="Xu, Ying" uniqKey="Xu Y" first="Ying" last="Xu">Ying Xu</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Biochemistry and Molecular Biology, Univ. of Georgia, 30602, Athens, GA</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Cai, Liming" sort="Cai, Liming" uniqKey="Cai L" first="Liming" last="Cai">Liming Cai</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Computer Science, Univ. of Georgia, 30602, Athens, GA</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="s" type="main" xml:lang="en">Lecture Notes in Computer Science</title><idno type="ISSN">0302-9743</idno><idno type="eISSN">1611-3349</idno><idno type="ISSN">0302-9743</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0302-9743</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity but also spatially conserved conformations caused by residue interactions, and consequently is computationally intractable. It is difficult to cope with the inefficiency without compromising alignment accuracy, especially for structure search in genomes or large databases. This paper introduces a novel method and a parameterized algorithm for structure-sequence alignment. Both the structure and the sequence are represented as graphs, where in general the graph for a biopolymer structure has a naturally small tree width. The algorithm constructs an optimal alignment by finding in the sequence graph the maximum valued subgraph isomorphic to the structure graph. It has the computational time complexity O(k t N 2) for the structure of N residues and its tree decomposition of width t. The parameter k, small in nature, is determined by a statistical cutoff for the correspondence between the structure and the sequence. The paper demonstrates a successful application of the algorithm to developing a fast program for RNA structural homology search.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Arkansas</li><li>Géorgie (États-Unis)</li></region></list><tree><country name="États-Unis"><region name="Géorgie (États-Unis)"><name sortKey="Song, Yinglei" sort="Song, Yinglei" uniqKey="Song Y" first="Yinglei" last="Song">Yinglei Song</name></region><name sortKey="Cai, Liming" sort="Cai, Liming" uniqKey="Cai L" first="Liming" last="Cai">Liming Cai</name><name sortKey="Huang, Xiuzhen" sort="Huang, Xiuzhen" uniqKey="Huang X" first="Xiuzhen" last="Huang">Xiuzhen Huang</name><name sortKey="Liu, Chunmei" sort="Liu, Chunmei" uniqKey="Liu C" first="Chunmei" last="Liu">Chunmei Liu</name><name sortKey="Malmberg, Russell L" sort="Malmberg, Russell L" uniqKey="Malmberg R" first="Russell L." last="Malmberg">Russell L. Malmberg</name><name sortKey="Song, Yinglei" sort="Song, Yinglei" uniqKey="Song Y" first="Yinglei" last="Song">Yinglei Song</name><name sortKey="Xu, Ying" sort="Xu, Ying" uniqKey="Xu Y" first="Ying" last="Xu">Ying Xu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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