2916019
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different approaches to the problem of identification. Consequently, it is difficult to maintain a consistent collection of pseudogenes in detail necessary for their effective use. Our database is designed to address this issue. It integrates a variety of heterogeneous resources and supports a subset structure that highlights specific groups of pseudogenes that are of interest to the research community. Tools are provided for the comparison of sets and the creation of layered set unions, enabling researchers to derive a current ‘consensus’ set of pseudogenes. Additional features include versatile search, the capacity for robust interaction with other databases, the ability to reconstruct older versions of the database (accounting for changing genome builds) and an underlying object-oriented interface designed for researchers with a minimal knowledge of programming. At the present time, the database contains more than 100 000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources.
29068146
PseudoPipe: an automated pseudogene identification pipeline
MOTIVATION
Mammalian genomes contain many 'genomic fossils' i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes.


RESULTS
We have developed a homology-based computational pipeline ('PseudoPipe') that can search a mammalian genome and identify pseudogene sequences in a comprehensive and consistent manner. The key steps in the pipeline involve using BLAST to rapidly cross-reference potential "parent" proteins against the intergenic regions of the genome and then processing the resulting "raw hits" -- i.e. eliminating redundant ones, clustering together neighbors, and associating and aligning clusters with a unique parent. Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts.
7503202
Proxy-assisted techniques for delivering continuous multimedia streams
We present a proxy-assisted video delivery architecture that can simultaneously reduce the resources requirements at the central server and the service latency experienced by clients (i.e., end users). Under the proposed video delivery architecture, we develop and analyze two novel proxy-assisted video streaming techniques for on-demand delivery of video objects to a large number of clients. By taking advantage of the resources available at the proxy servers, these techniques not only significantly reduce the central server and network resource requirements, but are also capable of providing near-instantaneous service to a large number of clients. We optimize the performance of our video streaming architecture by carefully selecting video delivery techniques for videos of various popularity and intelligently allocating resources between proxy servers and the central server. Through empirical studies, we demonstrate the efficacy of the proposed proxy-assisted video streaming techniques.
206417245
Estimation of Displacements from Two 3-D Frames Obtained From Stereo
A method for estimating 3D displacements from two stereo frames is presented. It is based on the hypothesize-and-verify paradigm used to match 3D line segments between the two frames. In order to reduce the complexity of the method, an assumption is made that objects are rigid. The formulate a set of complete rigidity constraints for 3D line segments and integrate the uncertainty of measurements in this formation. The hypothesize-and-verify stages of the method use an extended Kalman filter to produce estimates of the displacements and of their uncertainty. The algorithm is shown to work on indoor and natural scenes. It is also shown to be easily extended to the case in which several mobile objects are present. The method is quite robust, fast, and has been thoroughly tested on hundreds of real stereo frames. >
6709890
An agent-based hybrid framework for database mining
While knowledge discovery in databases (KDD) is defined as an iterative sequence of the following steps: data pre-processing, data mining, and post data mining, a significant amount of research in data mining has been done, resulting in a variety of algorithms and techniques for each step. However, a single data-mining technique has not been proven appropriate for every domain and data set. Instead, several techniques may need to be integrated into hybrid systems and used cooperatively during a particular data-mining operation. That is, hybrid solutions are crucial for the success of data mining. This paper presents a hybrid framework for identifying patterns from databases or multi-databases. The framework integrates these techniques for mining tasks from an agent point of view. Based on the experiments conducted, putting different KDD techniques together into the agent-based architecture enables them to be used cooperatively when needed. The proposed framework provides a highly flexible and robust data-mining platform and the resulting systems demonstrate emergent behaviors although it does not improve the performance of individual KDD techniques.
13014692
Extracting Reusable Object-Oriented Legacy Code Segments with Combined Formal Concept Analysis and Slicing Techniques for Service Integration
Web services, together with service-oriented architectures, are promising integration technology to facilitate legacy system Webification and evolution. However, a service-oriented re-engineering process is still essential for legacy systems to survive in the service-oriented computing environment. In this service-oriented re-engineering process, understanding and reusing object-oriented code turn to be important activities. In this paper, we proposed a comprehensive approach to support the extraction and integration of reusable object-oriented legacy code. In the extraction phase, formal concept analysis, which is a general and flexible technique for recovering structural design information, and inter-procedural program slicing are adopted as main reverse engineering techniques to recover reusable object-oriented code. In the integration phase, service packaging processes are presented in details. Our approach produces extracted components with core legacy object-oriented code function in Web services by wrapping underlying computing models with XML
5416143
A clustering based approach to efficient image retrieval
This paper addresses the issue of effective and efficient content based image retrieval by presenting a novel indexing and retrieval methodology that integrates color, texture, and shape information for the indexing and retrieval, and applies these features in regions obtained through unsupervised segmentation, as opposed to applying them to the whole image domain. In order to address the typical color feature "inaccuracy" problem in the literature, fuzzy logic is applied to the traditional color histogram to solve for the problem to a certain degree. The similarity is defined through a balanced combination between global and regional similarity measures incorporating all the features. In order to further improve the retrieval efficiency, a secondary clustering technique is developed and employed to significantly save query processing time without compromising the retrieval precision. An implemented prototype system has demonstrated a promising retrieval performance for a test database containing 2000 general-purpose color images, as compared with its peer systems in the literature.