Terminator sequence search in E.coli K12

Abstract

Under the circumstance of rapid progress of genome analyses, automatic identification of genes and operons, which are a set genes, are becoming still more important. The signal included in the operon may play an important role for identification of genes. Those signals are the terminator which is in the 3'-terminal of operon and Shine-Dalgarno sequence which is in the 5'-terminal of the operon. In the present report we developed the simple method for specifying terminators. The dot-matrix method, which has been used for the analysis of secondary structure of RNA, applied for the terminator sequence search with the free energy parameters as scores. Free energy parameters of Serra about successive base pairs were used. They were modified to adapt for experimentally identified terminators. Sixty nucleotides at the down stream of stop codon of all annotated E.coli K12 genes were extracted and used as candidates for terminators. Sequences with high score values included rich T regions, and low score sequences did not. It is conjectured that the former is the rho-independent terminator and the latter is the rho-dependent terminator.