2026-07-26T02:45:54Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:2687 2024-03-06T11:09:19Z ddc:004 open_access

Estimation of alternative splicing isoform frequencies from RNA-Seq data Nicolae, Marius Mangul, Serghei Mandoiu, Ion Zelikovsky, Alex RNA-Seq alternative splicing isoforms expectation maximization We present a novel expectation-maximization algorithm for inference of alternative splicing isoform frequencies from high-throughput transcriptome sequencing (RNA-Seq) data. Our algorithm exploits largely ignored disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information if available. Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Marius Nicolae and Serghei Mangul and Ion Mandoiu and Alex Zelikovsky 2010 Is Part Of Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/DagSemProc.10231.5 urn:nbn:de:0030-drops-26876 https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.5 eng https://creativecommons.org/licenses/by/4.0/legalcode