Alternative Splicing Detection Tool-a novel PERL algorithm for sensitive detection of splicing events, based on next-generation sequencing data analysis

Abstract

Next-generation sequencing (NGS) can provide researchers with high impact information regarding alternative splice variants or transcript identifications. However, the enormous amount of data acquired from NGS platforms make the analysis of alternative splicing events hard to accomplish. For this reason, we designed the "Alternative Splicing Detection Tool" (ASDT), an algorithm that is capable of identifying alternative splicing events, including novel ones from high-throughput NGS data. ASDT is available as a PERL script at http://aias.biol.uoa.gr/~mtheo and can be executed on any system with PERL installed. In addition to the detection of annotated and novel alternative splicing events from high-throughput NGS data, ASDT can also analyze the intronic regions of genes, thus enabling the detection of novel cryptic exons residing in annotated introns, extensions of previously annotated exons, or even intron retentions. Consequently, ASDT demonstrates many innovative and unique features that can efficiently contribute to alternative splicing analysis of NGS data.

Keywords: Bioinformatics; alternative splicing; isoform; next-generation sequencing (NGS); splice variant.

Figure 1

Schematic demonstration of ASDT output files. (A) ASDT output file demonstrating sequencing reads that match a single alternative splicing event. Each line corresponds to one record and shows the read ID, the sequencing read that represents it, the keyword that was matched and the exons that formed it; (B) ASDT output file demonstrating sequencing reads that match multiple alternative splicing events. The symbol “<--->” is used to represent the coexistence of alternative splicing events in a single sequencing read; (C) ASDT output file depicting sequencing reads that are predicted to contain novel cryptic exons, exon extensions or intron retentions. ASDT, Alternative Splicing Detection Tool.

Figure 2

ASDT output file providing a simple and quick overview of all the alternative splice junctions that were detected, including novel ones, as well as the number of occurrences each one was noticed. ASDT, Alternative Splicing Detection Tool.