Research On Gene Transcription Regulatory Motif Prediction And Its Online Service Development

Research on Bioinformatics field has proposed several interesting computationalproblems. The prediction of gene transcription regulatory motif is one of them. Motif isa group of short sequences, length about8-12bps, which can be consisted by DNAsequence, protein sequence and its structure. In the thesis, we research on predictiongene transcription regulatory motif in DNA sequence. It helps life science researchers tounderstand the mechanism in gene transcription regulatory, and make contributions tomedical, bioengineering, and other fields. The most commonly used methods of motifprediction are based on Heuristic Algorithm, for the work of recognition motif ismultiple sequences alignment problem, which is a NP complex problem. However, thecapability of these methods confronted the shortage of highly false positive rate. Inreality, the bioinformatics tools should be used in a lower false positive rate. The motifprediction method, named BoBro, which has been developed by our research group, cansolve the problem effectively. It used the similarity of each motif sequence to reduce“noise” signal in the background by the data processing technology. The mainly contentin the thesis is to introduce my work that make an online service to predict and analysisgene transcription regulatory motifs, in order to popularize BoBro method and newlyextended function. The web service is named DMINDA (http://csbl.bmb.uga.edu/DMINDA/).It provides the services to achieve:(1) calculate a statistic score with its statisticalsignificant P-value, using a set of target promoter sequences and its control data set.(2)Offer some new function, motif scan, compare and co-occurrence analysis to help theanalysis of predicted results.(3) Conveniently prepare the input data, a set of promotersequences, with the supported by a database (DOOR, a Database of prOkaryoticOpeRons) and Phylogenetic foot printing knowledge.In DMINDA system designing, it should have the knowledge in correspondingresearch beyond the software development skills to understand the actually needs ofusers. There are a lot of bioinformatics tools have not been widely used to reveal theirvalue. It’s an important research field in computer application technology to popularize these methods by using web design technology to make a web service. Someone calledit Science2.0. In the support by previous studies by our research group, my workachieves the parallelism running of the algorithm BoBro with the analysis tools for itsresults, deployed them on a highly computational cluster with150nodes. Additionally,we make a method based on Phylogenetic foot printing knowledge to predict motifs anda work pipeline to predict regulon in whole genome. Both of these papers are insubmitting. Making a web service to popularize our research can promote the level ofJournal our paper published and increase its influence factor. It also contributes to ourfuture research. The thesis mainly introduces my work in design, development andmaintenance for DMINDA web service, and reviews the prediction of genetranscription regulatory motif.