Conference Paper: T-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract)
| Title | T-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract) |
|---|---|
| Authors | Peng, Y1 Leung, HCM1 Yiu, SM1 Chin, FYL1 |
| Keywords | Alternative Splicing De Bruijn Graph De Novo Transcriptome Assembly Isoforms Next-Generation Sequencing |
| Issue Date | 2011 |
| Publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ |
| Citation | Lecture 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 |
| 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. |
| ISSN | 0302-9743 2011 SCImago Journal Rankings: 0.034 |
| DOI | http://dx.doi.org/10.1007/978-3-642-20036-6_31 |
| References | References in Scopus |
| dc.contributor.author | Peng, Y |
|---|---|
| dc.contributor.author | Leung, HCM |
| dc.contributor.author | Yiu, SM |
| dc.contributor.author | Chin, FYL |
| dc.date.accessioned | 2012-06-26T06:32:17Z |
| dc.date.available | 2012-06-26T06:32:17Z |
| dc.date.issued | 2011 |
| dc.description.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. |
| dc.description.nature | Link_to_subscribed_fulltext |
| dc.identifier.citation | Lecture 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.citeulike | 9394272 |
| dc.identifier.doi | http://dx.doi.org/10.1007/978-3-642-20036-6_31 |
| dc.identifier.epage | 338 |
| dc.identifier.issn | 0302-9743 2011 SCImago Journal Rankings: 0.034 |
| dc.identifier.scopus | eid_2-s2.0-79953209688 |
| dc.identifier.spage | 337 |
| dc.identifier.uri | http://hdl.handle.net/10722/152000 |
| dc.identifier.volume | 6577 LNBI |
| dc.language | eng |
| dc.publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ |
| dc.publisher.place | Germany |
| dc.relation.ispartof | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
| dc.relation.references | References in Scopus |
| dc.subject | Alternative Splicing |
| dc.subject | De Bruijn Graph |
| dc.subject | De Novo Transcriptome Assembly |
| dc.subject | Isoforms |
| dc.subject | Next-Generation Sequencing |
| dc.title | T-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome (Extended abstract) |
| dc.type | Conference_Paper |
Author Affiliations
- The University of Hong Kong