ABSTRACT
Dinucleotide Associations ..................................................................... 212 8.5 Visualization Tools for Splice Site Features ................................................................... 213 8.6 Spliceomics Applications in Genome Annotation ........................................................ 215 8.7 Statistical Modeling in Spliceomics................................................................................. 216
8.7.1 Entropy Modeling .................................................................................................. 216 8.7.1.1 Maximum Entropy Method .................................................................. 217 8.7.1.2 Constraints ............................................................................................... 217 8.7.1.3 Maximum Entropy Model ..................................................................... 218
8.7.2 Decision Trees ........................................................................................................ 218 8.7.3 Combinatorial Model ............................................................................................ 218
8.8 Tools and Databases .......................................................................................................... 219 8.8.1 Tools ......................................................................................................................... 219
8.8.1.1 Berkeley Drosophila Genome Project .................................................. 219 8.8.1.2 FSPLICE .................................................................................................... 219 8.8.1.3 GeneSplicer .............................................................................................. 219
Splicing is highly necessary for a typical eukaryotic mRNA before its translation to a correct protein. It involves a series of reactions that are catalyzed by the spliceosome. The spliceosome is a complex of small nuclear ribonucleoproteins (snRNPs) and protein subunits that removes introns from a transcribed pre-mRNA (hnRNA). There are also certain self-splicing introns that do not need the interference of spliceosomes. The RNA-splicing highly depends on the introns and they are classied on the basis of biochemical analysis of splicing reactions. At least four distinct classes of introns have been identied [1] and are discussed in the following subsections. A typical eukaryotic nuclear intron has consensus sequences dening important regions. Each intron has GU at its 5ʹ end, a branch site followed by a series of pyrimidines or a polypyrimidine tract (PPT), then by AG at the 3ʹ end [2]. Generally, the nucleotide A is always found at the branch point and the consensus around this sequence varies to some extent.
