Combinatorial Pattern Discovery Tool with Tutorial Module

Abstract

One of the problems arising in the analysis of biological sequences is the discovery of sequence similarity in the primary structure of related proteins or genes. Such similarity usually corresponds to residues conserved during evolution due to an important structural or functional role.

Currently there are some computer programs that find patterns in biological sequences such as protein/DNA/RNA sequences. The Combinatorial Pattern Discovery Tool with Tutorial Module aims to find maximal patterns given the input sequences and the required parameters using the Teiresias algorithm. The users of the system can browse through each of the maximal patterns and their corresponding offset list. The users can view the summary of results and they can also opt to save the summary of results in their hard disks. In addition, the Tutorial Module provides lectures and supplementary study materials to aid the users in understanding the concepts behind the discovery of patterns in biological sequences. A Flash animation file is included to demonstrate how the Teiresias algorithm works given a sample input. An automatically-generated self-test whose questions are taken from the database is also provided so that students can test their knowledge of the concepts.