Bioinformatics Tools: Searching for Markers in DNA/RNA Sequences

Research in bioinformatics and computational biology relies heavily on algorithms that facilitate the understanding of biological processes through the application of statistical and heuristic techniques. These techniques, due to the vast amount of data they process and inherent complexity of the algorithm they employ, are better handled by computers. In this paper, we introduce two tools developed in Java language specifically designed to help us analyze and comprehend two completely different problems in bioinformatics research. The first problem is to identify and record the frequencies of specific patterns (markers) in DNA sequences. The second problem is to analyze the probability of the formation of triplexes in miRNA sequence alignments by looking for matching base pairs. We hope that these tools or the ideas introduced in this paper can contribute to the ongoing research in computational biology and bioinformatics.

• Type: Conference
• Year: 2008
• Where: BIOCOMP
• Authors: Kuha Mahalingam, Omar Bagasra
• Keywords: BIOCOMP 2008, Bioinformatics, Computational Biology, Heuristic Techniques, MiRNA Sequence Alignments