termFall09 - CAP5510 Introduction to Bioinformatics Fall...

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1 CAP5510 Introduction to Bioinformatics Fall 2009 Term Projects Bioinformatics is a rapidly growing field. Several new research areas emerged just within the last 5 to 10 years. Some of these topics have already trickled down to graduate curriculum in several universities. With limited time in a semester, it is not possible to cover all these important topics. In the term project, several options will be given and you are supposed to choose one of them, as follows: A. Tutorial Paper : Choose one of the following topics and write a self-contained paper. 1. Proteomics and Protein Analysis 2. Genomic Analysis of RNA 3. Functional Genomics 4. Comparative Genomics and Genome Rearrangements 5. Human Genome 6. Structural Alignments 7. Bacteria and Archaea Genomes 8. Gene Expression: Microarray Data Analysis 9. Protein Sequencing and Mass Spectroscopy technology 10. High Throughput Genomic Sequence 11. SNPs (Single Nucleotide Polymorphism) and Variation B. Tools : Choose one of the major topics in Bioinformatics and find all the tools (except the tools that we have already discussed in the class like BLAST) available from important internet sites. You must include descriptions of the algorithms underlying these tools and need to research the papers where such descriptions were published. Explain the algorithms and then write a brief “user’s manual” describing how to use the tools and interpret the results. You must provide test runs (identify the relevant databases) of the tools with currently available biological databases for all the tools identified. C. Research Paper : Choose a research topic in Bioinformatics that might interest you, write a critical review of this field and then identify an open problem or an approach to improve the idea or the tool and then implement your own suggested improvement. The paper should be written in a professional style as if you are writing a chapter of a book or a technical paper for a conference, taking 10-15 pages (excluding Figures), in electronic form and a set of slides for presentation in the class based on the paper.
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2 CAUTION: You should try to write the chapter or the paper using your own language as much as possible. If you have to quote something or adopt a Figure from some source, you must acknowledge the source. Copying large parts from a source and pasting it in your paper can be detected easily. It is also illegal because it violates copyright laws and if such activities are found, your grade will be heavily penalized. Deadlines : November 2, 2009 : Submit a proposal outlining your project; identify the sources that you will use and a plan to execute the project.(maximum of two pages) November 16, 2009: Submit a first draft of your report electronically. November 18, 2009
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termFall09 - CAP5510 Introduction to Bioinformatics Fall...

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