Development of a BLAST-based command line tool for sequence alignment

Abstract

This thesis work studies the development of a BLAST (Basic Local Alignment Search Tool) -based command line tool for the use of biological sequence alignment. The focus of the work is in identifying the most important software quality criteria based on the target user base, and how to produce such a program using existing resources as efficiently as possible. The first part of the work covers the basic principles of biological sequence alignment, the BLAST algorithm, and related existing software applications. The next part introduces software quality criteria and typical models for their application. A brief literature review of the state of software development and quality in the field of bioinformatics is included to illustrate the most common problems that one might need to navigate in the development of a program such as the one discussed in this thesis. The second part of the thesis discusses the design of the program, selected quality criteria as well as technical aspects of the development. The results section details the results of the project with an overview of the program architecture. Following this is a discussion on how well the implementation filled the desired software quality criteria and ideas for further development.