Finished Projects for CMPS 243 Bioinformatics

1. Jim Kent Large scale C. briggsae/C. elegans genomic alignment shows interesting patterns of conservation, synteny and intron position
2. Terry Furey and Lilly Sprikovska Classification of Yeast Ribosomal Genes Using Upstream Region Patterns
3. Shuo Zhang, Huaizhi Wu, and Michael Wang Data analysis of molecule sequence
4. Charles Sugnet, Eric Rice, and Tyson Clark Rational Selection of Oligonucleotide Probes for Microarray Construction
5. Tyson Clark, Chi-Yip Ho, Scot Free Kennedy, and Charles Sugnet Micro array data normalization
6. Fan shen, Rong Gu, and Wei Ma Large-scale Promoter Analysis of Yeast Genes
7. Doug Whitmore Alignment Colorizer- using color to visualize uncertainty in protein sequence alignments
8. Matt Evans, Matt Xia, and Yuanwen Wu Novel Method for the Rapid Evaluation of Packing in Protein Structures
9. Thuylinh Nguyenle and Hui-Han Wu Thermus thermophilus 16S rRNA Secondary Structure Predictions
10. Eric Savage Extraction of Protein Structure for Protein Structure Prediction
11. Samuel K Handelman Hubbard Plots
12. Hong Luo Promoter Searching and Gene Finding. (Recommended to be viewed with Internet Explorer)
13. Steen Christensen, Valerie Phoung, and Mamta Rani Searching for regulatory elements of plant genes under Myb-related transcription factor control
14. Hui Wang An HMM Approach to Identify Novel Repeats Through Fluctuations in Composition
15. Guotao Lu and Pu Yang Gene Classification with Support Vector Machines
16. Brian Eaton Genetic Sequence Displayer
17. Eric Stawiski (Project will be available after data is published)
18. Leon Derman, Miriam Sivan-Zimet, and Steven Hallam Promoter Recognition Motif Search Extensible Engine
19. Dana Byrd Identification and Sequence Analysis of JSAP1 Homologs
20. Jennifer Compton (Project will be available after data is published)

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