The capstone to BIO/CSC 295 is a collaborative, interdisciplinary Final Project. Your goals are to
Ideally, the project will require significant contributions from both biology experts and computer science experts.
elevator presentationof your proposal in class.
Finding olfactory receptor genes. In order to write a program to find such receptors, one would first determine typical patterns of DNA that make it likely that the code for a receptor is nearby (biology expertise). One would then write a program that detects such patterns, handling possible variations and approximation (computer science expertise). Next, one would run the program to ensure that it identifies known olfactory receptor genes and to see if it also identifies new areas of the geneome that may code for olfactory receptors (mixed expertise).
Trans-membrane sequences. In addition to identifying alpha helices and beta sheets, can we identify other interesting structural characteristics? In particular, can we determine which part of a protein is likely to be a trans-membrane sequence? Biology expertise lets us identify and analyze data sets (and develops the question). CS expertise lets us adapt Chou-Fasman to this problem.
More generally, you may find it useful to try to adapt one of the techniques you've learned this semester to a need domain or data set. The last time we taught the course, one particularly ambitious group applied the Kellis technique to micro RNA sequences. You might find other applications for the Kellis approach, for Chou-Fasman-style techniques, for the Potti approach, and more.
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