PS5 - CH388 Fall 2007 (AY08-01) Problem Set #5...

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CH388 Fall 2007 (AY08-01) Problem Set #5 Bioinformatics (NCBI/BLAST) A Problem Set Submitted to: Instructor: _______________________ Hour: _________ In Partial Fulfillment of Requirements for CH388 Genetics By: Cadet ___________________________ *The formal group for this report does not include other cadets, classmates, or outside sources. Initials indicate: ______ My documentation attributes all sources used and assistance received in completing this assignment. ______ No sources were used or assistance received in completing this assignment. Signature _________________________________________ Date _________________________________________ United States Military Academy West Point, New York 1
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CH388 Fall 2007 (AY08-01) Problem Set #5 Bioinformatics (NCBI/BLAST) The following problem set is worth 75 points. Problems are due to the instructor NLT 1600 on 16 Nov 07. A Documentation of Written Work Coversheet must be initialed, signed, and attached. Any assistance outside of the instructor must be documented and properly acknowledged. This includes websites, textbooks, personnel and resources outside of original thought. For assistance or further guidance, see your instructor. Documentation for every answer must be included. What you include as a reference should be the actual last source that prompted your answer to the question. Improper/insufficient documentation will result in a decrement of points for each answer not adequately referenced. LEARNING TO USE BLAST: This tutorial is a more detailed look at the BLAST (Basic Local Alignment Search Tool) program at NCBI, the most important single software tool for searching sequence databases. BLAST can be used to query nucleic acids or proteins. This problem set will walk you through various portions of the NCBI bioinformatics and you should be familiar with its capabilities and organization. Type www.ncbi.nlm.nih.gov into your web browser. The page that appears is the National Center for Biotechnology Information (NCBI) home page. 1 Just below the title there is a row of subtitles of PubMed, All Databases, Blast, OMIM, etc., and just below those terms is a search box selected to All Databases. Place the mouse over the database pull-down menu and click to see a large list of databases linked through the NCBI site. Once you become familiar with the various databases you can quickly access them by selecting them from this list and hitting the return button. Notice the yellow list to links on the left-hand column of the homepage. At the top of this column is a link entitled “Site Map” followed by “About NCBI” and then “GenBank”. Place the mouse cursor over the link “About NCBI” and click. This is a link that
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This note was uploaded on 04/15/2008 for the course CH 388 taught by Professor Eslinger during the Fall '08 term at West Point.

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PS5 - CH388 Fall 2007 (AY08-01) Problem Set #5...

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