Predicting the Minimum Free Energy RNA Secondary Structures using Harmony Search Algorithm

The physical methods for RNA secondary structure prediction are time consuming and expensive, thus methods for computational prediction will be a proper alternative. Various algorithms have been used for RNA structure prediction including dynamic programming and metaheuristic algorithms. Musician's behaviorinspired harmony search is a recently developed metaheuristic algorithm which has been successful in a wide variety of complex optimization problems. This paper proposes a harmony search algorithm (HSRNAFold) to find RNA secondary structure with minimum free energy and similar to the native structure. HSRNAFold is compared with dynamic programming benchmark mfold and metaheuristic algorithms (RnaPredict, SetPSO and HelixPSO). The results showed that HSRNAFold is comparable to mfold and better than metaheuristics in finding the minimum free energies and the number of correct base pairs.

Parallezation Protein Sequence Similarity Algorithms using Remote Method Interface

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

A New Spectral-based Approach to Query-by-Humming for MP3 Songs Database

In this paper, we propose a new approach to query-by-humming, focusing on MP3 songs database. Since MP3 songs are much more difficult in melody representation than symbolic performance data, we adopt to extract feature descriptors from the vocal sounds part of the songs. Our approach is based on signal filtering, sub-band spectral processing, MDCT coefficients analysis and peak energy detection by ignorance of the background music as much as possible. Finally, we apply dual dynamic programming algorithm for feature similarity matching. Experiments will show us its online performance in precision and efficiency.