INDARE - An indexed DAG of regular expressions for selecting position frequency matrices

Abstract

The identification of putative motifs in biomolecular sequences or whole genomes/proteomes is frequently based on window-based scanning with position frequency matrices (PFMs). The exponential increase in the amount of sequence data and the growing number of patterns to be screened has resulted in the need for rapid screening methods. In recognition of this, we have developed the Indexed DAG of regular expressions extractor (INDARE), a tool that dynamically extracts regular expressions (REs) for each PFM in the database, and creates a directed acyclic graph of REs. The INDARE generated DAG is very effective in pruning the search space and easily outperforms the naive exhaustive sequential search approach. The method is general enough to be applicable for the identification of motifs in any domain.