Research Of Identification Of Alternative Promoters And Bidirectional Promoters Based On New-generation Sequencing Technology

The invention and the amazing progress of new-generation sequencing data laid agood foundation for the development of bioinformatics method and the recognization ofpromoter regions and transcription factor binding sites in the genome.Consequently, wecan illuminate and understand gene transcription regulation mechanism.It is improtant for understanding genome biological characteristics and their targetregulation to annotate the alternative promtoers. The annotation of alternative promoterscan be took advantage of prediction of the upstream regulatory regions and the sequencearound genes, as well as domain subunit. The bidirectional promtoers can regulate twodownstream genes. Some transcription factor binding sites in bidirectional promtoerregions influence the expression of the two genes in opposite directions. In addition, theabundance of the the bidirectional promoter construction has been observed acrossseveral mammalian genome, suggesting that there is evolutionary pressure for conservingthis type of gene-pair structure.Although there have been plenty of methods to recognize the promoter regions,because of the unique characteristics of regions, they are not appropriate forrecognization of alternative promtoer regions and bidirectional promoter regions. Themajor content of this paper consists of two parts, the recognization of alternativepromoters and the recognization of bidirectional promoters.The region expression pattern of alternative promoters and bidirectional promoterswere designed by their characteristics seperately. The PSO algorithm was used foroptimize the parameters of expression pattern. Then the promoter regions wererecognized in the genome. The recognization of alternative promtoer region adopted arelative value of promtoer region and intergenic region, whereas the model selectioncriterion was used to select the optimal model in the candidate models to recognize thebidirectional promoter regions.After that, DBTSS was took advantaged of examining theresult of alternative promtoer regions, and the simulation of the possible peak shape ofbidirectional promoter regions was used to verify the effectiveness of the method.The prediction of the alternative promoter regions could provide support for genomecharacteristics analyse including the relationship among the alternative promtoer regions and gene EST and the fragment of mRNA, and the conservation of alternative promtorregions. The recognization of bidirectional promoter regions could be used for exploringthe conversation of distance of two transcriptional start sites, the transcription regulationmachanism of two downstream genes and the relationship between the CpG island andthe bidirectional promtoer regions.