Cnit final presentation
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This document summarizes a CNIT final presentation about annotating the genome of the RiverMonster bacteriophage. It includes an introduction to bioinformatics and the goals of the CNIT course. It describes the bacteriophage and annotation tools used, including DNA Master, Phamerator, Glimmer, and GeneMark. It outlines the process of organizing the genome annotation between group members and analyzing each gene. It concludes with the accomplishments of completing the genome annotation and discusses the significance and potential future work.
Cnit final presentation
- 1. CNIT Final Presentation Chris Thompson April 18th, 2013 CNIT 227
- 2. Table of Contents Introduction Materials Methods Results and Conclusion
- 3. INTRODUCTION
- 4. Bioinformatics Bioinformatics – an interdisciplinary field that develops and improves upon methods for storing, retrieving, organizing, and analyzing biological data. Bioinformatics is important because without the technologies produced and developed through it, many of the experiments and assays we do today would not be possible.
- 5. CNIT CNIT is the bioinformatics course at Purdue, focused on annotating the genome of mycobacteriophages. Overall goal is to annotate the genome of the RiverMonster phage, so other researchers can use it in the future.
- 6. Bacteriophages • A virus that infects and replicates in bacteria • One of the most common and populous organism in existence • Many have a mosaic genome • Unlimited potential usage • Mycobacteriophages infect M.smegmatis
- 7. Clusters • System to organize bacteriophages • Phages sorted by factors such as genome length, presence of certain genes, organization of genome, GC content, and plaque size and characteristics • A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, Singleton, and T
- 8. RiverMonster • Discovered in 2010 in West Lafayette • Mycobacteriophage • Cluster E • 144 genes in total • Many protein products are unknown • Overall geographical presence is unknown Through CNIT and bioinformatics we are trying to answer some of the unknowns about RiverMonster
- 9. MATERIALS
- 10. Bioinformatics Tools • DNA Master • Phamerator • Glimmer • GeneMark • NCBI and BLAST • EverNote
- 11. DNA Master • Designed and written by Dr. Jeffrey Lawrence • Annotation program • Can auto-annotate entire genomes • Uses information from Glimmer and GeneMark • Can locally BLAST genes
- 12. Phamerator • Developed in 2011 • Linux-based bioinformatic program • Used for comparative phage genomics • Can visualize entire phage genomes • Separates phages into “phams”
- 13. Glimmer • Stands for Gene Locator and Interpolated Markov ModelER • Used for finding genes in microbial DNA • Uses models and algorithms to distinguish between coding and non-coding DNA
- 14. GeneMark • A family of gene prediction programs developed at the Georgia Institute of Technology • Determines the protein-coding potential of a DNA sequence • Uses many of the same algorithms and models as GIimmer
- 15. NCBI and BLAST • National Center for Biotechnology Information • Basic Local Alignment Search Tool • Program that compares DNA sequences with a large database of known sequences • Used to find similar gene sequences
- 16. EverNote • Started in 2008 • Designed for note-taking and archiving • Used as an online lab notebook for CNIT
- 17. METHODS
- 18. Organization • Genome split into two sections • Genes 0 to 65 by Jon and Bill • Genes 66 to 144 by Chris and Nyema • Split again into four sections • 0 to 23 by Jon • 24 to 65 by Bill • 100 to 123 by Chris • 124 to 144 by Nyema
- 19. Process • Document the auto-annotated gene call • Ran the Shine-Delgarno Test • BLASTed gene and compared scores • Compared homologous genes in Phamerator • Made final call
- 20. First Section • Genes 66 to 144 • Split up evens and odds • I had even numbered genes • No outstandingly tricky gene calls • Gene 88 seems to be a family of Kinases, many of them hypothetical • Gene 92 is a family of RNA ligases • Gene 94 is Transcription factor WhiB
- 21. Second Section • Genes 101 to 123 • Every gene • Gene 101 is a protease family • Gene 112 contains genes for polymerases • Genes 116 and 117 were reverse genes • 117 had many inconsistencies and was difficult to call
- 23. Accomplishments • Personally called 39 genes • Called 144 genes as a class • Analyzed protein products • Completed a final draft of the RiverMonster genome
- 24. Significance • Genome can be used by future scientists • Proves validity of undergraduate research • Learned about bioinformatics, bacteriophages, genomes, annotation, and biotechnology
- 25. Future Work • Check and finalize all gene calls • Compilation of DNA Master file • Send to HHMI and SEA Phages to be put in Phamerator
- 26. The End