NPCRIT: A novel protein coding region identifying tool using decision tree classifier with trust-region method & parallel scan algorithm

Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides that are found in DNA molecules. But, the regions of these genes that code for proteins may occupy only a small region of the sequence. Identifying the coding regions play a vital role in understanding these genes. In this paper we propose a NPCRIT tool for finding these protein coding regions which uses a Decision Tree Based classifier. This tool uses trust region method to find the closet (optimized) DNA nucleotide. It also uses a Sequential PRM-based protein folding algorithm for finding the point where these proteins add to the ladder. Standard parallel scan algorithm is used to provide parallel processing of the strides and its transitions. This proposed tool produces more accurate results, than that have previously been obtained for a range of different sequence lengths. Experimental results confirm the scalability of the proposed classifying tool to handle large volume of datasets irrespective of the number of classes, tuples and attributes. Good classification accuracy has been established.