Affiliation:
1. Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
2. Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
Abstract
Abstract
Summary
Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure. To address this issue and enable researchers to assess potential functional consequences of transcript isoform variation on the proteome, we developed IsoTV. IsoTV is a versatile pipeline to process, predict and visualize the functional features of translated transcript isoforms. Attributes such as gene and isoform expression, transcript composition and functional features are summarized in an easy-to-interpret visualization. IsoTV is able to analyze a variety of data types from all eukaryotic organisms, including short- and long-read RNA-seq data. Using Oxford Nanopore long read data, we demonstrate that IsoTV facilitates the understanding of potential protein isoform function in different cancer cell types.
Availability and implementation
IsoTV is available at https://github.molgen.mpg.de/MayerGroup/IsoTV, with the corresponding documentation at https://isotv.readthedocs.io/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
Max Planck Society
Fulbright Fellowship Grant
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability
Cited by
3 articles.
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