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

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

doi:10.1109/BIBMW.2011.6112351

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 proceeding › Conference 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 language	English (US)
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	26-33
Number of pages	8
DOIs	https://doi.org/10.1109/BIBMW.2011.6112351
State	Published - Dec 1 2011
Event	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States Duration: Nov 12 2011 → Nov 15 2011

Publication series

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

Other

Other	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Country	United States
City	Atlanta, GA
Period	11/12/11 → 11/15/11

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

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 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference 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, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, 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. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112351

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