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Conference Paper: T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome
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TitleT-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome
 
AuthorsPeng, Y1
Leung, HCM1
Yiu, SM1
Chin, FYL1
 
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/
 
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. 337-338 [How to Cite?]
DOI: http://dx.doi.org/10.1007/978-3-642-20036-6_31
 
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.
 
DescriptionLNCS v. 6577 entitled: Research in computational molecular biology: 15th annual international conference, RECOMB 2011 ... : proceedings
 
ISBN978-3-642-20035-9
 
ISSN0302-9743
2013 SCImago Journal Rankings: 0.310
 
DOIhttp://dx.doi.org/10.1007/978-3-642-20036-6_31
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorPeng, Y
 
dc.contributor.authorLeung, HCM
 
dc.contributor.authorYiu, SM
 
dc.contributor.authorChin, FYL
 
dc.date.accessioned2012-06-26T06:32:17Z
 
dc.date.available2012-06-26T06:32:17Z
 
dc.date.issued2011
 
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.
 
dc.description.naturepostprint
 
dc.descriptionLNCS v. 6577 entitled: Research in computational molecular biology: 15th annual international conference, RECOMB 2011 ... : proceedings
 
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. 337-338 [How to Cite?]
DOI: http://dx.doi.org/10.1007/978-3-642-20036-6_31
 
dc.identifier.citeulike9394272
 
dc.identifier.doihttp://dx.doi.org/10.1007/978-3-642-20036-6_31
 
dc.identifier.epage338
 
dc.identifier.hkuros187792
 
dc.identifier.isbn978-3-642-20035-9
 
dc.identifier.issn0302-9743
2013 SCImago Journal Rankings: 0.310
 
dc.identifier.scopuseid_2-s2.0-79953209688
 
dc.identifier.spage337
 
dc.identifier.urihttp://hdl.handle.net/10722/152000
 
dc.identifier.volume6577
 
dc.languageeng
 
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
 
dc.publisher.placeGermany
 
dc.relation.ispartofLecture Notes in Computer Science
 
dc.relation.referencesReferences in Scopus
 
dc.rightsThe original publication is available at www.springerlink.com
 
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License
 
dc.subjectNext-Generation Sequencing
 
dc.subjectIsoforms
 
dc.subjectDe Novo Transcriptome Assembly
 
dc.subjectDe Bruijn Graph
 
dc.subjectAlternative Splicing
 
dc.titleT-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome
 
dc.typeConference_Paper
 
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Author Affiliations
  1. The University of Hong Kong