A Red Aureus Genome-wide Range Of Cis Regulate The Prediction Research Of Binding Sites

Bioinformatics is the application of computer science and information technology to the field of biology and medicine, which uses computers as tools to store, search and analyze the bio-information. It is one of the newest interdisciplinary fields of life science and natural sciences; meanwhile it will be one of the most important core areas of natural sciences in the21st century. Its research priorities mainly reflected in two domains:genomics and proteomics. Specifically, it starts from the analysis of the nucleic acids and protein sequences to find out their expressive functions. In a genome, although its cis-regulatory binding sites and motifs formed by multiple adjacent binding sites are at least as important as its coding sequences, the traditional experimental methods will spend a lot of energy and time to identify them, which will limit our comprehension to the sequenced gene sequences, and will obstruct our knowledge and understanding of important biological processes. Biologists urgent need efficient and accurate algorithms and tools to predict the genome-wide cis-regulatory binding sites and motifs. They also need some database to store the motifs and their information to help them to decipher the cis-regulatory motif coding, and to prepare to find the secret code of human DNA. In this thesis we start with basic biologic knowledge, introduce DNA structure genes and transcription factors, and use the TF working mechanism to show the transcription factor binding sites prediction method. We also introduce a prokaryotic genome’s binding sites prediction algorithm, and use Perl as program language to find the transcription factor binding sites in Rhodococcus jostii RHA1. First we download the sequences form the GeneBank database and cut the upstream sequences sets, then use the motif finding algorithm to find the transcription factor binding sites, finally we do the motif similarity comparison to get the convincing results. Biologist can use our results to decipher the corynebacterineaes’ cis-regulatory encoding, to know and control the bacterium’s biological processes, or to produce some useful proteins or some anti-virus biopharmaceutical products.