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On Gene Prediction By Cross-Species Comparative Sequenced Analysis., Rong Chen
On Gene Prediction By Cross-Species Comparative Sequenced Analysis., Rong Chen
Student Work
The availability of large fragments of genomic DNA makes it possible to apply comparative genomics for identification of protein-coding regions. We have conducted a comparative analysis of homologous genomic sequences of organisms with different evolutionary distances and found the conservation of the non-coding regions between closely related organisms. In contrast, more distance shows much less intron similarity but less conversion on the exon structures. We sought to illuminate the impact of evolutionary distances on the performance of our gene-finding program based on the cross-species sequence comparison. Based on our finding and training of data sets, we proposed a model by …
Apd: The Multifunctional Antimicrobial Peptide Database And Analysis System., Zhe Wang
Apd: The Multifunctional Antimicrobial Peptide Database And Analysis System., Zhe Wang
Student Work
As of late 2003, more than 500 antimicrobial peptides have been reported. However, the majority data of the antimicrobial peptides are scattered in the literature. In order to better understand the structure-function relationship of these peptides, and antimicrobial peptide database and analysis system (APD) was established based on an extensive literature search. The database contains detailed information for 525 peptides (498 antibacterial , 155 antifungal, 28 antiviral, and 18 antitumor). Based on the database, the system also provides database query, statistical data, prediction and peptide design functions. APD provides web-based interfaces that allow users to visit the system via a …
A "Maximal Tree" Approach For Scheduling Tasks In A Multiprocessor System., Haiying Sun
A "Maximal Tree" Approach For Scheduling Tasks In A Multiprocessor System., Haiying Sun
Student Work
The problem of scheduling tasks across distributed system has been approved to be NP-complete in its general case. When communication cost among system processors is not considered, polynominal-time optimal algorithms for solving scheduling problem are exit only in three special cases. In attempting to solve the problem in the general case, a number of heuristics have been developed. These algorithms intend to reduce the input task graph to one of the special cases and then optimal scheduling can be obtained accordingly. In this paper, we study all these heuristics, and present a improved heuristic --- “Maximal Tree graph approach for …
Spatial Data Mining Using Branch Grafted R-Tree., Priyanka Dubey
Spatial Data Mining Using Branch Grafted R-Tree., Priyanka Dubey
Student Work
Spatial data mining is a process of extraction of implicit information, such as weather patterns around latitudes, spatial features in a region, et., with a goal of knowledge discovery. The existing spatial data mining methods typically identify a specific datamining task for knowledge discovery. An example of a mining task may involve finding weather patterns in the northwestern region of U.S.A. To find such weather patterns one could employ an existing data structure, such as a B+ tree followed by the analysis of the mined weather data for knowledge discovery. This is a typical top-down approach of identifying a task, …
Graph-Theoretic Approaches To Cluster Protein Sequences., Zhu Liu
Graph-Theoretic Approaches To Cluster Protein Sequences., Zhu Liu
Student Work
Finding homologous proteins (or cluster of homologous proteins) is a very important, since this information is required for nearly any further analysis of proteins. Two sequences are said to be homologous if they derive from a common ancestor. Generally, sequence similarity provides the base for the homology. There are several approaches to cluster proteins based on their homology. But very few methods involve graphic algorithms. In this project, five graph-based algorithms are implemented to cluster proteins. The five algorithms are finding strongly connected components (SCC) algorithm, finding partially strongly connected components (PSCC) algorithm, graph coloring algorithm, merging algorithm, random merging …
A Computational Approach To Reconstructing Gene Regulatory Networks., Xutao Deng
A Computational Approach To Reconstructing Gene Regulatory Networks., Xutao Deng
Student Work
Motivation: Many modeling frameworks have been applied to infer regulatory networks from gene expression data sets. Linear Additive Models (LAMs), as one large category of models, have been gaining more and more popularity. One problem associated with this kind of models is that the system is often under-determined because of excessive number of unknown parameters. In addition, the practical utility of these models has remained unclear. Methods: Based on LAMs, we developed an improved method to infer gene regulatory networks from time-series gene expression data sets. The method includes an incremental connectivity model with indexed regulatory elements and a linear …
An Evolutionary Approach To Routing In Mobile Ad Hoc Networks Using Dominating Sets., Hiranmayi Sreenivas
An Evolutionary Approach To Routing In Mobile Ad Hoc Networks Using Dominating Sets., Hiranmayi Sreenivas
Student Work
This thesis presents a new approach to routing in ad-hoc wireless networks using virtual backbones that may be approximated by the graph theoretic concept of dominating sets. · Ad hoc wireless networks provide a flexible and quick means of establishing wireless peer-to-peer communications. Routing remains the main challenging problem in an ad hoc network due to its multihop nature and dynamic network topology. Several protocols based on virtual backbones in ad hoc wireless networks have been proposed that may be used to simplify the routing process. However, little is known about the network routing performance of these protocols and no …
Vehicle Detection And Tracking By Computer Vision For Intelligent Transportation Applications., Peijun Shi
Vehicle Detection And Tracking By Computer Vision For Intelligent Transportation Applications., Peijun Shi
Student Work
The vehicle routing problem (VRP) deals with the allocation of vehicles to the customers that have requested products from a main depot. When the postal service, the bus system, or trucking industry plan for their everyday tasks of delivery goods or providing basic transportation needs to people, they are attempting to solve the VRP. However, this can be a daunting task because the VRP is computationally intensive. In this paper, we will address two areas of the VRP that have been relatively unexplored by previous research, yet play an important part in real-world_ applications of the VRP as well as …
An Evolutionary Approach To Vehicle Routing Problem With Dynamic Time And Precedence Relationships., Darin C. Plum
An Evolutionary Approach To Vehicle Routing Problem With Dynamic Time And Precedence Relationships., Darin C. Plum
Student Work
The vehicle routing problem (VRP) deals with the allocation of vehicles to the customers that have requested products from a main depot. When the postal service, the bus system, or trucking industry plan for their everyday tasks of delivery goods or providing basic transportation needs to people, they are attempting to solve the VRP. However, this can be a daunting task because the VRP is computationally intensive. In this paper, we will address two areas of the VRP that have been relatively unexplored by previous research, yet play an important part in real-world_ applications of the VRP as well as …