Tiger HRE Finder - A Tool for Identification of Hormone Receptor Binding Sites in Query Sequences

摘要

Prediction of transcription factor binding sites is a crucial challenge in investigation of mechanisms of gene expression regulation. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is difficult to establish an accurate model for recognition of functional regulatory elements in promoters of eukaryotic genes. Here we present a tool for precise prediction of a large group of transcription factor binding sites - steroid hormone response elements. The tool uses large training set of experimentally confirmed steroid hormone response elements, and adapts sequence-based statistic method of position weight matrix, for identification of the binding sites of the query sequences. Accuracy level (considering trade-off sensitivity vs. specificity) is a user-defined parameter and a table of correspondence of the above values is collected from a number of independent tests. The tool is freely available for academic and non-profit use http://birc.ntu.edu.sg/~pmaria.