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 Citations (Scopus)

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 - 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Other

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

Fingerprint

RNA
Transcriptome
Throughput
Messenger RNA

Keywords

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

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

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] https://doi.org/10.1109/BIBMW.2011.6112351

SPATA : A seeding and patching algorithm for de novo transcriptome assembly. / Zhao, Zhiyu; Nguyen, Tin Chi; Deng, Nan; Johnson, Kristen Marie; Zhu, Dongxiao.

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 26-33 6112351.

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

Zhao, Z, Nguyen, TC, Deng, N, Johnson, KM & 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., 6112351, pp. 26-33, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112351
Zhao Z, Nguyen TC, Deng N, Johnson KM, Zhu D. SPATA: A seeding and patching algorithm for de novo transcriptome assembly. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 26-33. 6112351 https://doi.org/10.1109/BIBMW.2011.6112351
Zhao, Zhiyu ; Nguyen, Tin Chi ; Deng, Nan ; Johnson, Kristen Marie ; Zhu, Dongxiao. / SPATA : A seeding and patching algorithm for de novo transcriptome assembly. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 26-33
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