Abstract—To enhance the speed and efficiency of structure based algorithms for protein Multiple Sequence alignment we need parallel processing. Secondary and tertiary structure of proteins are more important and informative then its primary structure. We get more accurate information’s about proteins when we conduct structure based matching. In this paper we have to focus on how to use parallel computing in terms of structure based algorithms. In case of protein structure based multiple sequence alignment several searches and structure matching are involved which require a lot of time and processing speed. If we use a parallel computer cluster or Grid then we can reduce processing time and get an optimal result. It will predict the function of protein from its structure.
Index Terms—APDB (A with PDB is used for ADP), BLAST, Cluster based on Mesh topology, DLT (Divisible load theory), FASTA, expresso, MPICH-G2, MPICH, PipeAlign, PRALINE, RMSD, Structure based Protein MSA, SGE, T-coffee, Taylor’s method.
Muhammad Ishaq Afridi and Yin Gui Sheng are with the College of Computer Science and Technology Harbin Engineering University, Harbin, Heilongjiang, China. (E-mail: ishaqafridipk@gmail.com; yinguisheng@hrbeu.edu.cn)
Cite: Muhammad Ishaq Afridi and Yin Gui Sheng, "Structure Based Protein Multiple Sequence Alignment Algorithm on a Parallel System," International Journal of Machine Learning and Computing vol. 2, no. 1, pp. 35-38, 2012.