Analysis of sequence patterns surrounding the translation initiation sites on Cyanobacterium genome using the hidden Markov model

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
T YadaM Hirosawa

Abstract

Sequence patterns surrounding the translation initiation sites of Cyanobacterium were precisely analyzed by the hidden Markov model (HMM) based on the actual translation initiation sites. In a previous study, 72 actual protein coding regions and their translation initiation sites on the genome of Synechocystis sp. strain PCC6803 were determined by Sazuka et al. using protein two-dimensional electrophoresis and microsequening. In this work, we extracted the sequence patterns surrounding translation initiation sites as HMM using the computer program YEBIS. The constructed HMM could recognize all but one translation initiation site. The HMM contains an AG-rich region (5.7 bp on average), as the Shine-Dalgarno sequence exclusively contains purines, upstream of the translation initiation site (-9.7 position on average) and a CT rich region (4.2 bp on average) just upstream from the translation initiation site. In addition, we found that the second amino acid (-4.5,6) could be classified into two types, one of which had C as their second codon while another of which has a nucleotide distribution relatively similar to the distribution among amino acids in the 72 proteins. This fact corresponds well to our earlier finding that when the...Continue Reading

Citations

Dec 15, 2006·BMC Structural Biology·Juliette MartinFrançois Rodolphe
Jun 30, 2000·Biochemical and Biophysical Research Communications·M JimboH Kamiya

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