Splice-Site Prediction

In Silico Technologies in Drug Target Identification and Validation 

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Predict the splice sites (acceptor and donor sites) of the above nucleotide sequence with WebGene or GenelD and SPL of Sanger Centre. Compare the results of their splice site predictions. 

Splice site prediction methods using a linear function that combines triplet preferences around splice junction and preferences to be coding and intron of adjacent regions have been developed [45, 61]. 692 sequences with... 

The general accuracy of acceptor site prediction was 96% (C = 0.47). Table 3.6 illustrates the performance for donor and acceptor sites and compares the results with the work of Mural et al. [60] who used triplet composition for splice site prediction, and the work of Brunak et al. [59] who used a complex neural network for site discrimination. 

SPL/splice site prediction (Human, Drosophila, Plants, Yeast) NetGene2/NetPGene/splice site... 

Hebsgaard, S. M., P. G. Koming, N. Tolstrup, J. Engelbrecht, R Rouze, and S. Brunak. 1996. Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information. Nucleic Acids Res 24 3439-52. 

Integrated Platforms for Gene, Promoter, and Splice Site Prediction Webgene http / / www. itba. mi. cnr.it/ webgene/... 

Splice site prediction tools will generally predict the functional impact of a polymorphism within close vicinity of a splice donor or acceptor site, although they will not predict the functional effect of polymorphisms in other elements, such as lariat branch sites. Definition of consensus motifs for these elements (fig. 4.5) makes it possible to assess the potential functional impact of polymorphisms in these gene regions by simply inspecting the location of a polymorphism in relation to the consensus motif. As with all functional predictions, laboratory investigation is required to confirm the hypothesis. 

Shown are nonsense, missense, deletion/insertion and splice site mutations. The amino acid changes are predictions in most cases. 

Detection of intron/exon splice sites Introns in eukaryotes cause discontinuation of the reading frame. If the analysis is not focused on a cDNA sequence, these introns must be spliced out and the exons joined to form the sequence that actually codes for the protein. Intron/exon splice sites can be predicted based on their common features. Most introns begin with the nucleotides GT and end with the nucleotides AG. There is a branch sequence near the downstream end of each intron involved in the splicing event. 

Coding sequences have characteristic features such as codon frequencies, start- and stop-codons, upstream TATA-boxes, and splice-sites, which can be used to annotate an ORF (14). While each piece of evidence is not, by itself, conclusive, the combination of factors can lead to firm identification of genes. Unfortunately this method is prone to a large number of false-positives, with at least 75% of predicted genes typically being artefacts (15). 

The SPL (search for potential splice sites) tool of the Sanger Centre predicts splice sites of an input query sequence. On the nucleotide sequence analysis page, paste the query sequence, enter the sequence name, select SPL tool, and click the... 

GenelD (Guigo, 1998) at http //wwwl.imim.es/software/geneid/index.html predict splice sites, codons, and exons along the query sequence using PWM. Exons are... 

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