MyJournals Home  

RSS FeedsAIDE: annotation-assisted isoform discovery with high precision [METHOD] (Genome Research)


2 december 2019 21:03:01

AIDE: annotation-assisted isoform discovery with high precision [METHOD] (Genome Research)

Genome-wide accurate identification and quantification of full-length mRNA isoforms is crucial for investigating transcriptional and posttranscriptional regulatory mechanisms of biological phenomena. Despite continuing efforts in developing effective computational tools to identify or assemble full-length mRNA isoforms from second-generation RNA-seq data, it remains a challenge to accurately identify mRNA isoforms from short sequence reads owing to the substantial information loss in RNA-seq experiments. Here, we introduce a novel statistical method, annotation-assisted isoform discovery (AIDE), the first approach that directly controls false isoform discoveries by implementing the testing-based model selection principle. Solving the isoform discovery problem in a stepwise and conservative manner, AIDE prioritizes the annotated isoforms and precisely identifies novel isoforms whose addition significantly improves the explanation of observed RNA-seq reads. We evaluate the performance of AIDE based on multiple simulated and real RNA-seq data sets followed by PCR-Sanger sequencing validation. Our results show that AIDE effectively leverages the annotation information to compensate the information loss owing to short read lengths. AIDE achieves the highest precision in isoform discovery and the lowest error rates in isoform abundance estimation, compared with three state-of-the-art methods Cufflinks, SLIDE, and StringTie. As a robust bioinformatics tool for transcriptome analysis, AIDE enables researchers to discover novel transcripts with high confidence.

110 viewsCategory: Bioinformatics, Genetics, Genomics
Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing [METHOD] (Genome Research)
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci [RESOURCES] (Genome Research)
blog comments powered by Disqus
The latest issues of all your favorite science journals on one page


Register | Retrieve



Copyright © 2008 - 2020 Indigonet Services B.V.. Contact: Tim Hulsen. Read here our privacy notice.
Other websites of Indigonet Services B.V.: Nieuws Vacatures News Tweets Nachrichten