University of Kentucky
Research Experience in Bioinformatics for Undergraduates
Institution
University of Kentucky
Faculty Advisor/ Mentor
Jerzy Jaromcyzk; Chuck Staben
Abstract
The Basic Local Alignment Search Tool (BLAST) is a sequence comparison algorithm used to search sequence databases for alignments of some portion of nucleic acid or protein sequences. This is a compute-intensive operation that can take from several minutes to hours depending on the computer that runs it. During the summer of 2004, as a part of the Research Experience in Bioinformatics for Undergraduates at UK, we participated in extending and testing the software for BooleanBlast. While BLAST allows for a search of only a single sequence, BooleanBlast adds the functionality to use queries of arbitrary complexity. For example it can process queries such as, "find sequence A AND sequence B OR sequence C, BUT NOT sequence D," et cetera. With the BooleanBlast, it is possible to create and use expressive BLAST queries based on Boolean combinations. Our group of Bioinformatics for Undergraduates focused on testing and providing user friendly graphical interfaces (GUIs). We developed and implemented for BooleanBlast two complete user interfaces, one similar to a traditional search engine, the other giving the user a more guided experience. In the process of adding these interfaces, the internal code of BooleanBlast was significantly tested and improved. As a result of the Summer Bioinformatics Program for Undergraduates, BooleanBlast offers a search tool with an intuitive GUI that is both flexible and powerful.
Research Experience in Bioinformatics for Undergraduates
The Basic Local Alignment Search Tool (BLAST) is a sequence comparison algorithm used to search sequence databases for alignments of some portion of nucleic acid or protein sequences. This is a compute-intensive operation that can take from several minutes to hours depending on the computer that runs it. During the summer of 2004, as a part of the Research Experience in Bioinformatics for Undergraduates at UK, we participated in extending and testing the software for BooleanBlast. While BLAST allows for a search of only a single sequence, BooleanBlast adds the functionality to use queries of arbitrary complexity. For example it can process queries such as, "find sequence A AND sequence B OR sequence C, BUT NOT sequence D," et cetera. With the BooleanBlast, it is possible to create and use expressive BLAST queries based on Boolean combinations. Our group of Bioinformatics for Undergraduates focused on testing and providing user friendly graphical interfaces (GUIs). We developed and implemented for BooleanBlast two complete user interfaces, one similar to a traditional search engine, the other giving the user a more guided experience. In the process of adding these interfaces, the internal code of BooleanBlast was significantly tested and improved. As a result of the Summer Bioinformatics Program for Undergraduates, BooleanBlast offers a search tool with an intuitive GUI that is both flexible and powerful.