Amreen Hossain will defend her master's project "A Comparative Analysis of BLAST Algorithms for Sequence Alignment," on Tuesday, August 30, 2016, at 5 p.m. in 256C Avery Hall. Her advisor was Dr. Jitender Deogun and committee members were Dr. Massimiliano Pierobon and Dr. Ashok Samal.
DNA sequencing is one of the most important problems in bioinformatics because querying helps in finding similar sequences in existing databases. Hence there have been many algorithms invented for DNA sequencing. BLAST is the most popular method of sequence searching. Currently there are many applications of the BLAST algorithm of which NCBI-BLAST is the most commonly used and deemed to be the most accurate. However, other applications claim to offer faster speeds for BLASTing while achieving the same accuracy as NCBI-BLAST. This project extensively studies several BLAST applications and they are analyzed using these metrics: speed, memory usage, accuracy, and user friendliness.
The focus of the project was to compare these BLAST techniques against NCBI BLAST and discover advantages, if any, these tools may have over NCBI BLAST. The tools that were analyzed were: AB BLAST, FSA BLAST, HS-BLASTN, MPI BLAST and NCBI-BLAST. These applications were tested on the Tusker cluster of the HCC system at the University of Nebraska-Lincoln.