SPATA: A seeding and patching algorithm for de novo transcriptome assembly

Zhiyu Zhao, Tin Chi Nguyen, Nan Deng, Kristen Marie Johnson, Dongxiao Zhu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.

Original languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages26-33
Number of pages8
DOIs
StatePublished - Dec 1 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

Other2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Keywords

  • RNA-seq
  • de novo assembly
  • read mapping
  • transcriptome

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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    Zhao, Z., Nguyen, T. C., Deng, N., Johnson, K. M., & Zhu, D. (2011). SPATA: A seeding and patching algorithm for de novo transcriptome assembly. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 26-33). [6112351] (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112351