Protein Sequence Analysis
Determination of amino acid sequence of protein, the study of the conformation changes of proteins and also the study of the complex molecules with any other non-peptide molecule is protein sequence analysis. The cellular processes of a living organism are known by the discovery of the structure and function of proteins, thus allowing researcher to develop and design drug targets. Mass-spectrometry and Edman degradation are the major methods to determine the protein sequencing. They have a principle advantage by following expansive quantities of proteins in parallel, which are additionally quick, mechanized, practical, profoundly touchy, and sparing examples and reagents. At this point, it is a promising methodology with a wide assortment of utilizations for experimental and clinical exploration.
Apart from maintaining the large database, mining useful information from these set of primary and secondary databases is very important. Lot of efficient algorithms have been developed for data mining and knowledge discovery. These are computation intensive and need fast and parallel computing facilities for handling multiple queries simultaneously. It is these search tools that integrate the user and the databases. One of the widely used search program is BLAST (Basic Local Alignment Search Tool).
BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits. BLAST uses a heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect relationships among sequences which share only isolated regions of similarity. This is a primary criterion in sequence analysis. Other tool available includes CLUSTALW for multiple sequence alignment.
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Journal of Next Generation Sequencing & Applications
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