Fast Database Indexing for Large Protein Sequence Collections Using Parallel N-Gram Transformation Algorithm

With the rapid development in the field of life sciences and the flooding of genomic information, the need for faster and scalable searching methods has become urgent. One of the approaches that were investigated is indexing. The indexing methods have been categorized into three categories which are the lengthbased index algorithms, transformation-based algorithms and mixed techniques-based algorithms. In this research, we focused on the transformation based methods. We embedded the N-gram method into the transformation-based method to build an inverted index table. We then applied the parallel methods to speed up the index building time and to reduce the overall retrieval time when querying the genomic database. Our experiments show that the use of N-Gram transformation algorithm is an economical solution; it saves time and space too. The result shows that the size of the index is smaller than the size of the dataset when the size of N-Gram is 5 and 6. The parallel N-Gram transformation algorithm-s results indicate that the uses of parallel programming with large dataset are promising which can be improved further.

Teaching Approach and Self-Confidence Effect Model Consistency between Taiwan and Singapore Multi-Group HLM

This study was conducted to explore the effects of two countries model comparison program in Taiwan and Singapore in TIMSS database. The researchers used Multi-Group Hierarchical Linear Modeling techniques to compare the effects of two different country models and we tested our hypotheses on 4,046 Taiwan students and 4,599 Singapore students in 2007 at two levels: the class level and student (individual) level. Design quality is a class level variable. Student level variables are achievement and self-confidence. The results challenge the widely held view that retention has a positive impact on self-confidence. Suggestions for future research are discussed.

Providing On-Demand Path and Arrival Time Information Considering Realtime Delays of Buses

This paper demonstrates the bus location system for the route bus through the experiment in the real environment. A bus location system is a system that provides information such as the bus delay and positions. This system uses actual services and positions data of buses, and those information should match data on the database. The system has two possible problems. One, the system could cost high in preparing devices to get bus positions. Two, it could be difficult to match services data of buses. To avoid these problems, we have developed this system at low cost and short time by using the smart phone with GPS and the bus route system. This system realizes the path planning considering bus delay and displaying position of buses on the map. The bus location system was demonstrated on route buses with smart phones for two months.

A System to Integrate and Manipulate Protein Database Using BioPerl and XML

The size, complexity and number of databases used for protein information have caused bioinformatics to lag behind in adapting to the need to handle this distributed information. Integrating all the information from different databases into one database is a challenging problem. Our main research is to develop a tool which can be used to access and manipulate protein information from difference databases. In our approach, we have integrated difference databases such as Swiss-prot, PDB, Interpro, and EMBL and transformed these databases in flat file format into relational form using XML and Bioperl. As a result, we showed this tool can search different sizes of protein information stored in relational database and the result can be retrieved faster compared to flat file database. A web based user interface is provided to allow user to access or search for protein information in the local database.

Fuzzy Join Dependency in Fuzzy Relational Databases

The join dependency provides the basis for obtaining lossless join decomposition in a classical relational schema. The existence of Join dependency shows that that the tables always represent the correct data after being joined. Since the classical relational databases cannot handle imprecise data, they were extended to fuzzy relational databases so that uncertain, ambiguous, imprecise and partially known information can also be stored in databases in a formal way. However like classical databases, the fuzzy relational databases also undergoes decomposition during normalization, the issue of joining the decomposed fuzzy relations remains intact. Our effort in the present paper is to emphasize on this issue. In this paper we define fuzzy join dependency in the framework of type-1 fuzzy relational databases & type-2 fuzzy relational databases using the concept of fuzzy equality which is defined using fuzzy functions. We use the fuzzy equi-join operator for computing the fuzzy equality of two attribute values. We also discuss the dependency preservation property on execution of this fuzzy equi- join and derive the necessary condition for the fuzzy functional dependencies to be preserved on joining the decomposed fuzzy relations. We also derive the conditions for fuzzy join dependency to exist in context of both type-1 and type-2 fuzzy relational databases. We find that unlike the classical relational databases even the existence of a trivial join dependency does not ensure lossless join decomposition in type-2 fuzzy relational databases. Finally we derive the conditions for the fuzzy equality to be non zero and the qualification of an attribute for fuzzy key.

A New Technique for Progressive ECG Transmission using Discrete Radon Transform

The aim of this paper is to present a new method which can be used for progressive transmission of electrocardiogram (ECG). The idea consists in transforming any ECG signal to an image, containing one beat in each row. In the first step, the beats are synchronized in order to reduce the high frequencies due to inter-beat transitions. The obtained image is then transformed using a discrete version of Radon Transform (DRT). Hence, transmitting the ECG, leads to transmit the most significant energy of the transformed image in Radon domain. For decoding purpose, the receptor needs to use the inverse Radon Transform as well as the two synchronization frames. The presented protocol can be adapted for lossy to lossless compression systems. In lossy mode we show that the compression ratio can be multiplied by an average factor of 2 for an acceptable quality of reconstructed signal. These results have been obtained on real signals from MIT database.

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.