CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

Due to the advancements in technology number of entries in the structural database of proteins are increasing day by day. Methods for retrieving protein tertiary structures from this large database is the key to comparative analysis of structures which plays an important role to understand proteins and their function. In this paper, we present fast and accurate methods for the retrieval of proteins from a large database with tertiary structures similar to a query protein. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods comes from the two newly introduced features, the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient and from the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/.

Solving the Minimum Common String Partition Problem with the Help of Ants

In this paper, we consider the problem of finding a minimum common partition of two strings. The problem has its application in genome comparison. As it is an NP-hard, discrete combinatorial optimization problem, we employ a metaheuristic technique, namely, MAX-MIN ant system to solve this problem. To achieve better efficiency we first map the problem instance into a special kind of graph. Subsequently, we employ a MAX-MIN ant system to achieve high quality solutions for the problem. Experimental results show the superiority of our algorithm in comparison with the state of art algorithm in the literature. The improvement achieved is also justified by standard statistical test.