TAAU: A tool to study the amino acid usage in different organisms

Worldwide there are scientists and researchers who deal with proteins in an attempt to find valuable information about the various species of organisms present on earth. With the expansion of available biological data, analysis is a major challenge facing researchers wishing to explore the massive amount of information. This paper presents the features of TAAU, a tool to study the amino acid usage in protein sequences. The analysis tools can be applied to either the protein sequences of different species or different proteins families. The tool allows the user to either download protein sequence information and files from online databases or to browse locally for a file or even to copy and paste a sequence for performing calculations like Grand Average of Hydropathy (GRAVY), the Codon Adaptation index (CAI) and frequency of amino acids amongst others. The results of the various analyses will be presented in the form of graphs and phylogenetic trees. TAAU has been implemented using Java, BioJava, PostgreSQL, JMoI, ClustalW, JFreeChart, JeUtils, and TreeView. The data have been organized in six (6) PostgreSQL tables to represent information pertaining to protein files, protein details, alignment of protein sequences and log files.