Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances b...

An evolutionary computation technique, genetic programming, was used to create programs that classify DNA sequences into one of three classes: (1) contains a centrally-located donor splice site, (2) contains a centrally-located acceptor splice site, and (3) contains neither donor nor an acceptor. The performance of the programs created are competitive with previous work.

We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein ...

We propose a new system for predicting the splice form of Caenorhabditis elegans genes. As a first step we generate a clean set of genes from available exressed sequence tags (EST) and complete complementary (cDNA) sequences. From all such genes we then generate potential acceptor and donor sites as they would be required by any gene finder. This leads to a clean set of true and decoy splice si...

Alternative splicing of transcripts in a signal-dependent manner has emerged as an important concept to ensure appropriate expression of splice variants under different conditions. Binding of the general splicing factor U2AF to splice sites preceding alternatively spliced exons has been suggested to be an important step for splice site recognition. For splicing to proceed, U2AF has to be replac...

BACKGROUND We previously described the use of tailed oligonucleotides as a means of reprogramming alternative pre-mRNA splicing in vitro and in vivo. The tailed oligonucleotides that were used interfere with splicing because they contain a portion complementary to sequences immediately upstream of the target 5' splice site combined with a non-hybridizing 5' tail carrying binding sites for the h...