Nov 29 2009
What we’ve learned in Bioinformatics
Topics, Concepts & Skills:
Overall
An idea of the scope and limitations of bioinformatics.
An ability to blog/make a website, create links and imbed images/videos.
Muscular dystrophy
History of muscular dystrophy and related diseases.
Understanding of role of cytogenetics and bioinformatics in identifying the Dystrophin. This includes chromosome banding/ideograms. Cellular role of Dystrophin in relation other proteins that cause DMD and other dystrophies, including LGMD. Relation of severity of genetic defect to disease phenotypes. Other assays used in studying muscular dystrophies.
Use of OMIM to learn about locations and functions of various components of the Dystroglyan Complex.
Experience with PDB files of protein structures.
The Human Genome Project and DNA sequencing
Understanding of the process of Genome Sequencing and Annotation, including new developments that have accelerated sequencing. Topics studied include base calling/issues with sequence quality and coverage, assembly of BAC clones into a Contig, finishing, annotation.
Appreciation of the historical significance of the Human Genome Project and the international collaborative nature of the project. Role of Hierarchical vs. Whole-genome sequencing in the final project. Read and wrote about the beginning sections of the HGP’s 2001 Nature Paper.
Touched upon or used PHRED, PHRAP, Sequencher.
Familiarity with the work of Craig Venter on the Human Genome Project and the JCVI’s recent research directions, including the Global Ocean Sampling Expedition, Marine Microbe Genome Sequencing Project, Synthetic Biology for microbes and vaccines, identification of entire new families of protein domains.
Gene Detection and Genome Annotation
Hands on experience with Gene Calling and Annotation (finding related genes), using the bacteriophage Eagle genome.
Dot plots and the role of visual analysis in understanding genomes.
Differences in prokaryotic vs. eukaryotic genes and the effect of those differences on Gene Detection. Methods used in gene annotation.
HIV Project
Read and understand primary literature. Explained a primary paper in a journal club format.
Developed and explored a unique bioinformatics question using original data from the HIV paper.
Some experience with new software, its power, and its limitations. The software includes Biology Workbench, Biology Student Workbench, SWAMI, ClustalW, and in one case MEGA4. Other tools used include Align, Grol4, MView, MEME.
Built phylogenic trees. Learned that file formats can make or break you.
Presented unique project in a class presentation and as a paper.
Multiple Alignments and Phylogenic Trees
Learned about different types of trees, their parts and what they can tell you. Touched upon how to pick the correct sequence to use in making a tree (synteny & orhtologs), theoretical approaches, synonymous and non-synonymous sites. Using fast-mutating vs. highly conserved sequences.
SMS Project
Met a graduate student author of a bioinformatics paper. Learned about the complex disease Smith-Magenis Syndrome.
Learned about clinical features of SMS and diagnostic methods related to bioinformatics. Journal Club of an original paper using the array comparative genomic hybridization technique. Analysis/critique of results and data presentation.
Original Project using data from SMS paper or RAI1 gene sequences. Presented in paper format.
Genome structure: repeats, SNPs, CNVs.
