Abstract
Alternative Splicing (AS) is the molecular phenomenon whereby multiple transcripts are produced from the same gene locus. As a consequence, it is responsible for the expansion of eukaryotic transcriptomes. Aberrant AS is involved in the onset and progression of several human diseases. Therefore, the characterization of exon–intron structure of a gene and the detection of corresponding transcript isoforms is an extremely relevant biological task. Nonetheless, the computational prediction of AS events and the repertoire of alternative transcripts is yet a challenging issue.
Hereafter we introduce PIntron, a software package to predict the exon-intron structure and the full-length isoforms of a gene given a genomic region and a set of transcripts (ESTs and/or mRNAs). The software is open source and available at http://pintron.algolab.eu. PIntron has been designed for (and extensively tested on) a standard workstation without requiring dedicated expensive hardware. It easily manages large genomic regions and more than 20,000 ESTs, achieving good accuracy as shown in an experimental evaluation performed on 112 well-annotated genes selected from the ENCODE human regions used as training set in the EGASP competition.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Caceres J, Kornblihtt A (2002) Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet 18:186–193
Pirola Y et al (2012) PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text. BMC Bioinformatics 13:S2
Bonizzoni P et al (2009) Detecting alternative gene structures from spliced ESTs: a computational approach. J Comput Biol 16:43–66
Green RE et al (2003) Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19(S1):i118–i121
Bonizzoni P, Rizzi R, Pesole G (2005) ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics 6:244
Djebali S, Delaplace F, Crollius HR (2006) Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biol 7(Suppl 1):S7
Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292
Bonizzoni P et al (2009) Minimum factorization agreement of spliced ESTs. Lectures Notes in Bioinformatics (LNCS). Proceedings of 9th workshop on algorithms in bioinformatics WABI, vol 5724. pp 1–12
Sheth N et al (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 34:3955–3967
GuigĂł R et al (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 7(Suppl 1):S2
Burset M, Seledtsov I, Solovyev V (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res 28:4364–4375
Zhang H et al (2005) PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res 33(Suppl 1):D116–D120
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Bonizzoni, P., Vedova, G.D., Pesole, G., Picardi, E., Pirola, Y., Rizzi, R. (2015). Transcriptome Assembly and Alternative Splicing Analysis. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2291-8_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2290-1
Online ISBN: 978-1-4939-2291-8
eBook Packages: Springer Protocols