Identifying the binding sites and promoters in the genomes remains one of the most research topics in computational biology in past ten years. In the upstream region of the start codon, there exist transcription and translation motifs whose distances and patterns vary among different genomic sequences. However, the existing computational approaches for detecting them are mostly general-purpose. For archaea, binding motifs are almost undiscovered as they are more hidden than bacteria or eukaryotes. In this report, an improved algorithm based on PWM (position-weight matrix) and Gibbs Sampler was proposed for finding any number of patterns in a given range. Experiments using this algorithm were done to detect the potential binding motifs in archaeal genomic sequences, and the results were analyzed among different settings and species. The comparison with biological experiments result shows that the improved algorithm is feasible to find more significant patterns for archaea than the traditional approaches.
transcription and translation in prokaryotes pdf download
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