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Conference Paper: T-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract)
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TitleT-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract)
 
AuthorsPeng, Y1
Leung, HCM1
Yiu, SM1
Chin, FYL1
 
KeywordsAlternative Splicing
De Bruijn Graph
De Novo Transcriptome Assembly
Isoforms
Next-Generation Sequencing
 
Issue Date2011
 
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
 
CitationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2011, v. 6577 LNBI, 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.
 
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.naturelink_to_subscribed_fulltext
 
dc.identifier.citationLecture Notes In Computer Science (Including Subseries Lecture Notes In Artificial Intelligence And Lecture Notes In Bioinformatics), 2011, v. 6577 LNBI, 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.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 LNBI
 
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 (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
 
dc.relation.referencesReferences in Scopus
 
dc.subjectAlternative Splicing
 
dc.subjectDe Bruijn Graph
 
dc.subjectDe Novo Transcriptome Assembly
 
dc.subjectIsoforms
 
dc.subjectNext-Generation Sequencing
 
dc.titleT-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract)
 
dc.typeConference_Paper
 
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Author Affiliations
  1. The University of Hong Kong