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1. Consider the sequence GAACTCATACGAATTCACGTCAGCCCATCGTGCCACGTCreate a %(G+C) plot of this sequence. On the y axis will be %(G+C) and on the x axis will be the nucleotide sequence number. Use a sliding window of 3 nucleotides and slide the window 1 nucleotide at a time. Calculate the %G+C as a function of nucleotide sequence number. You may use an Excel spreadsheet to create the plot. Change the sliding window to 5 nucleotides and create a second plot. Overlap the two plots. Show your instructor the spread sheet and the graph. 2. Given the following sequence: PLSQETFSDLWKLLPENNVLSP use the Kyte/Doolittle Hydropathy scale and a sliding window of 7 amino acids to construct a hydropathy plot. Use an Excel spreadsheet for this exercise. 3. Find the protein sequence for bacteriorhodopsin from purple bacteria. Make sure you obtain the full-length sequence. Find the Kyte-Doolittle Hydropathy program in the Bioinformatics Tools site. Perform Kyte-Doolittle analysis of bacteriorhodopsin. Compare the plot to the one displayed in lecture today. Are there differences in the two plots? If so, why? 4. Import the human p53 (Accession number AAH03596) and squid p53 (Accession number AAA98563) sequences from the protein database at NCBI onto your hard drive in FASTA format. This can be accomplished by changing the display format on the ENTREZ screen to FASTA. Highlight the entry and copy onto clipboard. Open NotePad on your local hard drive. Paste each sequence into a separate document and save them in a folder named "sequence" in the Temp folder on C drive. Name the documents p53_human and p53_squid. Use the Dotter program on your hard drive to compare p53_human.txt with p53_human.txt Do you detect some parallel lines in the dot plot? Why? What does the greyramp tool do? Capture the image and save.. Type dotter c:\sequence\p53_human.txt c:\sequence\p53_squid.txt RETURN What are the differences between the human vs. human comparison and the human vs. squid comparison? |
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