A Multilevel Secure Relational Database Model with key-polyinstantiation

Thumbnail Image
Date
2006-01-01
Authors
Stakhanova, Natalia
Dhingra, Ruchi
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract

The problem of recognizing motifs from biological data has been well-studied and numerous algorithms, both exact and approximate, have been proposed to address the underlying issue. We strongly believe that open availability and ease of accessibility of quality implementations for such algorithms are critical to the research community, in order to directly reproduce and utilize the results from other studies, so as not to reinvent the wheel. Moreover, it is also important for the implementation to be as generic as possible so that any researcher can to extend it with minimal effort to test a newly implemented algorithmic extension or heuristic. With this motivation, we choose to focus an existing algorithm, PatternBranching and, to a lesser degree, Yang2004. We analyze these approaches for minor heuristical changes & speed-ups by adjusting certain thresholds, and finally, implement the variant in high-level language (Java) using thought through programming practices and generic, extensible interfaces. We also analyze the performance of PatternBranching using a synthetically generated test-suite for a variety of sequence lengths and report the results. Code from this project will be made freely available online to the research community.

Series Number
Journal Issue
Is Version Of
Versions
Series
Academic or Administrative Unit
Type
article
Comments
Rights Statement
Copyright
Funding
Subject Categories
DOI
Supplemental Resources
Source
Collections