RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes

Serghei Mangul; Adrian Caciula; Ion Mandoiu; Alex Zelikovsky

doi:10.1109/BIBMW.2011.6112363

RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes

Serghei Mangul^*, Adrian Caciula, Ion Mandoiu, Alex Zelikovsky

^*Corresponding author for this work

Surgery, Thoracic Surgery Division

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

4 Scopus citations

Abstract

We describe the problem of transcriptome reconstruction in partially annotated genomes from RNA-Seq that involves unannotated transcripts discovery and reconstruction in the context of incomplete annotation. In this paper we present an annotation-guided transcriptome reconstruction method and compare it with existing annotation-guided and genome-guided assemblers. Our Detection and Reconstruction of Unannotated Transcripts (DRUT) method is used to enhance existing transcriptome assemblers. Our method enables accurate detections of reads from unannotated transcripts and applying transcriptome assembler on subset of reads improve reconstruction quality. Empirical analyses on synthetic datasets show that enhancement of existing transcriptome assemblers with DRUT can increase number of assembled transcripts from RNA-Seq data.

Original language	English (US)
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	118-123
Number of pages	6
DOIs	https://doi.org/10.1109/BIBMW.2011.6112363
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

Conference

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

Keywords

alternative splicing
expectation maximization
RNA-Seq
transcriptome reconstruction

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

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Mangul, S., Caciula, A., Mandoiu, I., & Zelikovsky, A. (2011). RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 118-123). [6112363] (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112363

Mangul, Serghei ; Caciula, Adrian ; Mandoiu, Ion ; Zelikovsky, Alex. / RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 118-123 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

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Mangul, S, Caciula, A, Mandoiu, I & Zelikovsky, A 2011, RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112363, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 118-123, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112363

RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. / Mangul, Serghei; Caciula, Adrian; Mandoiu, Ion; Zelikovsky, Alex.

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 118-123 6112363 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Mangul S, Caciula A, Mandoiu I, Zelikovsky A. RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 118-123. 6112363. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112363