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Full-Text Articles in Computer Engineering

Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope Dec 2009

Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope

Computer Science and Engineering: Theses, Dissertations, and Student Research

Reconstructing the evolutionary history of biological sequences will provide a better understanding of mechanisms of sequence divergence and functional evolution. Long-term sequence evolution includes not only substitutions of residues but also more dynamic changes such as insertion, deletion, and long-range rearrangements. Such dynamic changes make reconstructing sequence evolution history difficult and affect the accuracy of molecular evolutionary methods, such as multiple sequence alignments (MSAs) and phylogenetic methods. In order to test the accuracy of these methods, benchmark datasets are required. However, currently available benchmark datasets have limitations in their sizes and evolutionary histories of the included sequences are unknown. These ...


Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet Nov 2009

Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet

Computer Science and Engineering: Theses, Dissertations, and Student Research

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are currently over 1100 molecular biology databases dispersed throughout the Internet. However, very few of them integrate data from multiple sources. To assist in the functional and evolutionary analysis of the abundant number of novel proteins, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database that integrates data from various biological sources. PROFESS is freely available athttp://cse.unl.edu/~profess/. Our database is designed to be versatile and ...


Deployed Software Analysis, Madeline M. Diep May 2009

Deployed Software Analysis, Madeline M. Diep

Computer Science and Engineering: Theses, Dissertations, and Student Research

Profiling can offer a valuable characterization of software behavior. The richer the characterization is, the more effective the client analyses are in supporting quality assurance activities. For today's complex software, however, obtaining a rich characterization with the input provided by in-house test suites is becoming more difficult and expensive. Extending the profiling activity to deployed environments can mitigate this shortcoming by exposing more program behavior reflecting real software usage. To make profiling of deployed software plausible, however, we need to take into consideration that there are fundamental differences between the development and the deployed environments. Deployed environments allow for ...