| Title: | Multiple Sequence Alignment |
| Course: | Algorithms for Bioinformatics (CPSC 545) |
| Timeframe: | 09.2004 - 01.2005 |
| Supervisor: | Holger Hoos |
| Abstract: | Multiple sequence alignment of proteins or nucleic acids is an important aspect of many bioinformatics applications, but it is a difficult problem. In this project, we studied two global iterative refinement methods using the sum-of-pairs score as our objective function: PRRP and A*-DCA. We evaluated our implementations and the programs by comparing our alignments with those provided in the BAliBASE reference sets. We found that PRRP and A*-DCA were similar in their ability to align equidistance and equi-homology sequence sets, to handle extension/insertion of blocks of sequences. Using simulated evolution, we also found that the two programs were similar in handling evolutionary changes. These results were expected since both programs are similar in nature: both iterative and global. |
| Team: | I did this project with another CS graduate student - Heidi Lam. |
| Language: | Java 1.5 |
| Downloads: | Paper (PDF) [800 KB], Source (ZIP) [110 KB] |
minevskiy
gmail.com
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