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Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista

  • Sylvain Foissac
  • Michael Sammeth
Part of the Methods in Molecular Biology book series (MIMB, volume 1269)

Abstract

Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process is highly regulated and makes up a large part of the differences between species, cell types, and states. The key to compare AS across different genes or organisms is to tokenize the AS phenomenon into atomary units, so-called AS events. These events then usually are grouped by common patterns to investigate the underlying molecular mechanisms that drive their regulation. However, attempts to decompose loci with AS observations into events are often hampered by applying a limited set of a priori defined event patterns which are not capable to describe all AS configurations and therefore cannot decompose the phenomenon exhaustively.

In this chapter, we describe working scenarios of AStalavista, a computational method that reports all AS events reflected by transcript annotations. We show how to practically employ AStalavista to study AS variation in complex transcriptomes, as characterized by the human GENCODE annotation. Our examples demonstrate how the inherent and universal AStalavista paradigm allows for an automatic delineation of AS events in custom gene datasets. Additionally, we sketch an example of an AStalavista use case including next-generation sequencing data (RNA-Seq) to enrich the landscape of discovered AS events.

Key words

Gene expression RNA processing Alternative splicing AS event Definition of alternative splicing Transcriptome annotation RNA-seq Splicing nomenclature AS code Bioinformatics 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.UMR1388 GenPhySEFrench National Institute for Agricultural Research (INRA)Castanet TolosanFrance
  2. 2.BioinformaticsNational Laboratory of Cientific Computing (LNCC)PetropolisBrazil

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