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080820.ProblemSet1 - PMCB PCB 5530 Due email before 9:30AM...

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PMCB – PCB 5530 PROBLEM SET 1 Due 9/1/2008 email before 9:30AM to [email protected] 12.5 Points Total 1. (4 pts) Explain ALL of the evidence that Cohen and Boyer used in their seminal work to prove that they produced, for the first time, recombinant DNA molecules in vitro . Cohen, Chang, Boyer, Helling (1973) PNAS 70 (11): 3240-3244 Morrow, Cohen, Chang, Boyer, Goodman, Helling (1974) PNAS 71 (5): 1743- 1747 2. (8.5 pts for all 16 questions) INTRODUCTION TO ON-LINE RESOURCES IN BIOINFORMATICS by Kathy Osteryoung (Michigan State University) as modified by K. Cline and J. Davis (University of Florida) This exercise is an introduction to the tools of bioinformatics. The term bioinformatics refers broadly to the application of computing and statistical methods to the management of large databases of biological information, particularly information being generated by the numerous genome sequencing programs now underway. The tools of bioinformatics consist of a wealth of computer programs, accessible via the Internet, which can be used for analysis of specific genes and/or proteins of interest, and for accessing the huge amount of available sequence information in a variety of ways. These tools have become an indispensable component of the research being conducted in almost every modern laboratory in cell biology, molecular biology and genetics. They are used on a daily basis for analyzing and comparing sequence data as well as for identifying new genes. In this exercise, you will use a variety of on-line programs to: Retrieve nucleotide and protein sequence and other information from online databases Assemble clusters of EST sequences into contiguous sequences (contigs). Translate DNA into protein sequences Conduct BLAST similarity searches to identify sequences that are similar to a sequence of interest Conduct multiple sequence alignments Identify potential subcellular targeting signals Go through the exercise, recording the sequences you obtain and the first Hit of each BLAST search. Answer all of the questions, which are numbered!!! The Context: You study disease resistance in Pinus species. Much is known about pathogenesis in model plant species, notably Arabidopsis thaliana . You would like to know if pine responds to pathogens in a similar way as Arabidopsis responds to pathogens. The Exercise: As a start, you are asking the question “Does pine produce the pathogenesis related protein called PR-1?” The first part of this exercise will involve a number of activities conducted with NCBI (National Center for Biotechnology Information) databases and analysis programs
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PMCB – PCB 5530 PROBLEM SET 1 Step A. Retrieving the Arabidopsis sequence for PR-1 Go to the ENTREZ browser at http://www.ncbi.nlm.nih.gov/Entrez/ Type ‘Arabidopsis pathogenesis related protein 1 (PR-1)’ into the search window and press Go .
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