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Conference Paper: T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome

TitleT-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome
Authors
KeywordsNext-Generation Sequencing
Isoforms
De Novo Transcriptome Assembly
De Bruijn Graph
Alternative Splicing
Issue Date2011
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), Vancouver, BC., Canada, 28-31 March 2011. In Lecture Notes in Computer Science, 2011, v. 6577, p. 337-338 How to Cite?
Abstract
RNA-seq data produced by next-generation sequencing technology is a useful tool for analyzing transcriptomes. However, existing de novo transcriptome assemblers do not fully utilize the properties of transcriptomes and may result in short contigs because of the splicing nature (shared exons) of the genes. We propose the T-IDBA algorithm to reconstruct expressed isoforms without reference genome. By using pair-end information to solve the problem of long repeats in different genes and branching in the same gene due to alternative splicing, the graph can be decomposed into small components, each corresponds to a gene. The most possible isoforms with sufficient support from the pair-end reads will be found heuristically. In practice, our de novo transcriptome assembler, T-IDBA, outperforms Abyss substantially in terms of sensitivity and precision for both simulated and real data. T-IDBA is available at http://www.cs.hku.hk/~alse/ tidba/. © 2011 Springer-Verlag.
DescriptionLNCS v. 6577 entitled: Research in computational molecular biology: 15th annual international conference, RECOMB 2011 ... : proceedings
Persistent Identifierhttp://hdl.handle.net/10722/152000
ISBN
ISSN
2013 SCImago Journal Rankings: 0.310
References

 

DC FieldValueLanguage
dc.contributor.authorPeng, Yen_US
dc.contributor.authorLeung, HCMen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorChin, FYLen_US
dc.date.accessioned2012-06-26T06:32:17Z-
dc.date.available2012-06-26T06:32:17Z-
dc.date.issued2011en_US
dc.identifier.citationThe 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), Vancouver, BC., Canada, 28-31 March 2011. In Lecture Notes in Computer Science, 2011, v. 6577, p. 337-338en_US
dc.identifier.isbn978-3-642-20035-9-
dc.identifier.issn0302-9743en_US
dc.identifier.urihttp://hdl.handle.net/10722/152000-
dc.descriptionLNCS v. 6577 entitled: Research in computational molecular biology: 15th annual international conference, RECOMB 2011 ... : proceedings-
dc.description.abstractRNA-seq data produced by next-generation sequencing technology is a useful tool for analyzing transcriptomes. However, existing de novo transcriptome assemblers do not fully utilize the properties of transcriptomes and may result in short contigs because of the splicing nature (shared exons) of the genes. We propose the T-IDBA algorithm to reconstruct expressed isoforms without reference genome. By using pair-end information to solve the problem of long repeats in different genes and branching in the same gene due to alternative splicing, the graph can be decomposed into small components, each corresponds to a gene. The most possible isoforms with sufficient support from the pair-end reads will be found heuristically. In practice, our de novo transcriptome assembler, T-IDBA, outperforms Abyss substantially in terms of sensitivity and precision for both simulated and real data. T-IDBA is available at http://www.cs.hku.hk/~alse/ tidba/. © 2011 Springer-Verlag.en_US
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/en_US
dc.relation.ispartofLecture Notes in Computer Scienceen_US
dc.rightsThe original publication is available at www.springerlink.com-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectNext-Generation Sequencingen_US
dc.subjectIsoformsen_US
dc.subjectDe Novo Transcriptome Assemblyen_US
dc.subjectDe Bruijn Graphen_US
dc.subjectAlternative Splicingen_US
dc.titleT-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptomeen_US
dc.typeConference_Paperen_US
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailChin, FYL: chin@cs.hku.hken_US
dc.identifier.authorityLeung, HCM=rp00144en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.description.naturepostprinten_US
dc.identifier.doi10.1007/978-3-642-20036-6_31en_US
dc.identifier.scopuseid_2-s2.0-79953209688en_US
dc.identifier.hkuros187792-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79953209688&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume6577en_US
dc.identifier.spage337en_US
dc.identifier.epage338en_US
dc.publisher.placeGermanyen_US
dc.identifier.scopusauthoridChin, FYL=7005101915en_US
dc.identifier.scopusauthoridYiu, SM=7003282240en_US
dc.identifier.scopusauthoridLeung, HCM=35233742700en_US
dc.identifier.scopusauthoridPeng, Y=30267885400en_US
dc.identifier.citeulike9394272-
dc.customcontrol.immutablesml 140923-

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