A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

Abstract

Background: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing only occurs under specific biological conditions. Non-expression based computational methods support identification of rarely expressed transcripts.

Results: A non-expression based statistical method is presented to annotate alternatively spliced exons using a single genome sequence and evidence from cross-species sequence conservation. The computational method is implemented in the program ExAlt and an analysis of prediction accuracy is given for Drosophila melanogaster.

Conclusion: ExAlt identifies the structure of most alternatively spliced exons in the test set and cross-species sequence conservation is shown to improve the precision of predictions. The software package is available to run on Drosophila genomes to search for new cases of alternative splicing.

Figure 1

Three forms of alternative splicing: Intron Retention (IR), Cassette Exon (CE), and Multiple Splice sites (MS).

Figure 2

Alternative and single isoform exon candidates. Four splice sites are shown, one acceptor a₀, and three donor sites, d₀, d₁, and d₂, and the begin (B) and end (E) of the input sequence. There are four candidate constitutive exons (Constitutive Exon), three candidate cassette exons (Cassette Exon), and candidate exons with multiple functional donor sites (Multiple Splice Site Exon). See text for a description of the splice types: single acceptor (SA), cassette acceptor (CA), single donor (SD), cassette donor (CD), multiple donor 1 (MD1), multiple donor 2 (MD2), and multiple donor above two in number (MDN).

Figure 3

Left image shows a portion of the graphical model for alternatively spliced exons. The right side of the figure shows two examples of parsing a target sequence. The top right example parses an intron retention sequence and the bottom right example parses a multiple splice site sequence. Blue states output partial subsequence of alternatively spliced exons, beige states are exons beginning with an acceptor and ending with a donor. Green states are introns.

Figure 4

Phylogenetic tree for four species of Drosophila. Each branch i has a branch length of b_i.

Figure 5

Model from Figure 3 expanded to include alternative splicing in terminal and initial exons and candidate single exon genes. Blue and beige states reflect possible protein coding exons (beige) or partial protein coding exons (blue) and represent three states for each state shown, one for each of the three coding phases. Special states "Beg" and "End" show the respective begin and end states in the model.