Promatch: A Computational Method for Identifying Conserved Transcription Factor Binding Sites in C. Elegans. (Revised)

The nematode species C. Elegans serves as an ideal model organism for genomic research due to the simplicity of its genetic structure when compared to most vertebrates. Study of C. Elegans has served to identify many target genes of several regulatory transcription factors. It has been shown through prior research that the transcription factor binding sites which have the largest effect on gene expression tend to be conserved across the genomes of several different species. Using this knowledge, we will utilize the level of species conservation into an accessible format that will allow researchers around the world to enhance their genomic studies. We have developed such a method to incorporate the conservation of DNA sequences across six different nematode genomes into a mathematical algorithm. These include the genomes of: C. Elegans, C. Briggsae, C. Japonica, C. Remanei C. Brenneri, and P. Pacificus. This algorithm has the ability to identify specific transcription factors using position weight matrices obtained through the TRANSFAC database which are significantly represented in a submitted C Elegans gene list. This algorithm will be presented to the public through a website where one may submit a list of genes and choose from one of three background models.