A multi-agent system simulating human splice site recognition

An approach of encoding for prediction of splice sites using SVM

In splice sites prediction, the accuracy is lower than 90% though the sequences adjacent to the splice sites have a high conservation. In order to improve the prediction accuracy, much attention has been paid to the improvement of the performance of the algorithms used, and few used for solving the fundamental issues, namely, nucleotide encoding. In this paper, a predictor is constructed to predict the true and false splice sites for higher eukaryotes based on support vector machines (SVM). Four types of encoding, which were mono-nucleotide (MN) encoding, MN with frequency difference between the true sites and false sites (FDTF) encoding, Pair-wise nucleotides (PN) encoding and PN with FDTF encoding, were applied to generate the input for the SVM. The results showed that PN with FDTF encoding as input to SVM led to the most reliable recognition of splice sites and the accuracy for the prediction of true donor sites and false sites were 96.3%, 93.7%, respectively, and the accuracy for predicting of true acceptor sites and false sites were 94.0%, 93.2%, respectively.

p53 intronic point mutation, aberrant splicing and telomeric associations in a case of B-chronic lymphocytic leukaemia

We report a case of chronic lymphocytic leukaemia (CLL) with telomeric associations and a p53 intronic point mutation. Karyotypic analysis revealed clonal and non-clonal telomeric associations, accompanied by clonal cytogenetic abnormalities and also in isolation. The p53 mutation, which occurred at the invariant base pair -2 of the splice acceptor site in intron 7 resulted in the abolition of correct splicing of exon 7 to exon 8. Multiple aberrant splice products were characterized, all of which differed from wildtype in the DNA binding domain. Fluorescence in situ hybridization demonstrated that the clone retained two copies of the p53 gene and wild-type p53 transcript was detected on cloning of reverse transcriptase polymerase chain reaction (RT-PCR) product, indicating that one wild-type allele remained. However, a plasmid clone with correct splicing at the exon 7/8 boundary, but with a 21 bp deletion in exon 8, was also found at low frequency. This finding indicates clonal evolution, resulting in complete loss of wild-type p53. The intronic point mutation was not present in DNA extracted from cervical tissue indicating that it was a leukaemic phenomenon. This is the first case of an intronic point mutation to be reported in CLL. This mutation led to chaotic p53 expression and, interestingly, occurred in a case showing telomeric associations, a rare phenomenon in B-CLL.