Results A method for predicting trans-splicing sites must be able to identify more than one likely splice site in a given trans-splicing region if the conditions warrant such a prediction. Otherwise, the predictive ability of the method would be limited to identifying one of several possible splice sites. Therefore, we wished to assess our method’s predictive ability on a set of known trans-spl...

The regulatory and accessory proteins of human immunodeficiency virus type 1 (HIV-1) are produced from singly or multiply spliced mRNAs. We have used HIV-1-specific oligonucleotide primer pairs in a polymerase chain reaction procedure on RNA from lymphocyte cell lines infected with HIV-1(228,200). The amplified products were analysed by hybridization with splice junction-specific oligonucleotid...

We present a novel classification method for splice sites prediction using support vector machine (SVM). The method first represents input sequences by sequence-based features, including the information of the distribution of tri-nucleotides and the conserved features surrounding the splice sites characterized by Markov model. An F-score based feature selection method is then used to select inf...

The use of antisense oligonucleotides to modulate splicing patterns has gained increasing attention as a therapeutic platform and, hence, the mechanisms of splice-switching oligonucleotides are of interest. Cells expressing luciferase pre-mRNA interrupted by an aberrantly spliced beta-globin intron, HeLa pLuc705, were used to monitor the splice-switching activity of modified oligonucleotides by...

The influenza virus M1 mRNA has two alternative 5' splice sites: a distal 5' splice site producing mRNA3 that has the coding potential for 9 amino acids and a proximal 5' splice site producing M2 mRNA encoding the essential M2 ion-channel protein. Only mRNA3 was made in uninfected cells transfected with DNA expressing M1 mRNA. Similarly, using nuclear extracts from uninfected cells, in vitro sp...

It is known that while the programs used to predict genes are good at determining coding nucleotides, there are considerable inaccuracies in the determination of the gene structural elements. Among them, the most notable is that of the exact boundaries of exons. In order to assess this, we had earlier reviewed various programs that predict potential splice sites and exons. The results led to th...

Alternative splicing (AS) constitutes a major mechanism creating protein diversity in humans. Previous bioinformatics studies based on expressed sequence tag and mRNA data have identified many AS events that are conserved between humans and mice. Of these events, approximately 25% are related to alternative choices of 3' and 5' splice sites. Surprisingly, half of all these events involve 3' spl...

Effective splice site selection is critically controlled by flanking splicing regulatory elements (SREs) that can enhance or repress splice site use. Although several computational algorithms currently identify a multitude of potential SRE motifs, their predictive power with respect to mutation effects is limited. Following a RESCUE-type approach, we defined a hexamer-based 'HEXplorer score' as...

Alternative splicing (AS) constitutes a major mechanism creating protein diversity in humans. Previous bioinformatics studies based on expressed sequence tag and mRNA data have identified many AS events that are conserved between humans and mice. Of these events, 25% are related to alternative choices of 30 and 50 splice sites. Surprisingly, half of all these events involve 30 splice sites that...

In Drosophila melanogaster, the fruitless (fru) gene controls essentially all aspects of male courtship behavior. It does this through sex-specific alternative splicing of the fru pre-mRNA, leading to the production of male-specific fru mRNAs capable of expressing male-specific fru proteins. Sex-specific fru splicing involves the choice between alternative 5' splice sites, one used exclusively ...