Performance and scalability evaluation of short fragment sequence alignment applications

Abstract

Mapping short fragments to open access eukaryotic genomes at a very large scale presents a data processing challenge to the scientific world. The main tool used for such an application is BLAST which is the one we use in our portlets developed at Obuda University. Lately most of our work has been focused on evaluating the performance and scalability of our applications by profiling, analyzing the results of the tests and improving the performance of both the portlets and the server-side massively parallel algorithm by environment optimization using the data collected during the testing phase. In this paper we will describe the two portlets (Deep Aligner and Disease Gene Mapper), discuss the issues and challenges during the development and the performance analysis and present our results on the performance and scalability of the applications.