Deriving Ribosomal Binding Site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction

摘要

Accurate prediction of the position of translation initiation (N-terminal prediction) is a difficult problem. N-terminal prediction from DNA sequence alone is ambiguous if several candidate start sites are close to each other. Protein similarity search is usually unable to indicate the true strat of a gene as it would require a strong protein sequence similarity at the N-terminal protion of a protein where conservative regions are rarions are rarely situated. With the aid of the GeneMark program for gene identification, we extract DNA sequence fragments presumably containing ribosome binding sites (RBS) from unannotated complete genomic sequences. These DNA segments are aligned to generate the RBS model using the Gibbs' sampling method. N-terminal prediction is then performed by using the RBS model in conjunction with the GeneMark start codon prediction to aid in determining the true Nt-erminal site.