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

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages118-123
Number of pages6
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

Conference

Conference2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Keywords

  • alternative splicing
  • expectation maximization
  • RNA-Seq
  • transcriptome reconstruction

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Fingerprint Dive into the research topics of 'RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes'. Together they form a unique fingerprint.

Cite this