Splice junctions

Figure shows a consensus sequence for a typical eukaryote gene. We can see that in the exon-intron junctions there is great similarity to the consensus sequence (i.e. the frequencies there are close to 100%).

  

Figure: Intron-Exon splice junctions [].

The figure shows an anchor point in the intron called branch point that appears frequently. Another statistical characteristic is a pyrimidine (bases C,T) rich area that appears between the branchpoint and the acceptor site. This naturally leads to using algorithms based on position specific weight matrices. This idea does not exploit all the information (reading frames, intron/exon states, etc) and is not suitable for short genes. Consequently, we will look for integrated approaches.