Dhaka University Journal of Applied Science & Engineering

One of the major challenges in bioinformatics is to characterize novel protein sequences. It is determined by making comparison with known protein sequences stored in protein sequence databases and family databases. Protein sequences are compared mainly by means of sequence alignments. Now days, various bioinformatics pattern-recognition methods have been developed to encode conserved regions in the sequence alignments. These conserved regions are used to characterize particular protein families, which in turn highlights the function and structure of member protein’s. This study concerns an investigation of a range of bioinformatics services, databases and software available on the Web in characterizing a novel protein sequence and its function. The potency of these bioinformatics tools has been assessed by identifying a retinal protein bacteriorhodopsin (BR) of the archaeon Halobacterium salinarum. lt is a transmembrane protein found in the cellular membrane of these organisms and functions as a light driven proton pump.

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