Plan of action

The main goal of the project will be to implement a user interface to GBA, enabling biologists and other semi-technical folk to easily utilize the algorithm. Two methods, web-based and standalone, will be investigated. The choice of implementation language will depend on factors such as ease of implementation, speed, and compatibility with original implementation language. The author will perform experiments, verifying that the results of the original algorithm implementation and the results exhibited by the user interface match, using a selection of data from the Swiss-Prot database.

As a secondary goal of the project, the author will investigate shortcomings of GBA in an attempt to improve upon the algorithms. Particularly, resultant LCRs that should appear as one continuous LCR occasionally appear as a scattered, broken lengths of smaller LCRs. Alternate methods of LCR sequence extension (a.k.a. following vertex edges in GBA) may provide insight into the fragmentation problem, leading to a novel solution. Experiments comparing the resultant LCRs of the original and altered algorithms will determine the ability of the new algorithm to solve the older algorithm’s LCR segmentation inconsistencies. Again, the Swiss-Prot database will provide the data used to test the altered algorithm.