Texas A&M University



BLAST Homework 12 points Do not print out your results! Only provide the information to answer the questions. This sequence is not actually from the NCBI database. GTGTCTTTGCGGGACGGACTGTGTGTGTCTTTGCGGGACGGACTGTGTTCCTCCAGAGAGCCCGTGAGTACACTGTCCAAGAGGTTTGAGAGAAGCGAGACGCTAACCGAAGCAGTGGACTGTTACCGGTGTCTTTGCGGGACGGACTGTGTTCCTCCAGAGAGCCCGTGAGTACACTGTCCAAGAGGTTTGAGAGAAGCGAGACGCTAACCGAAGCAGTGGACTGTTACCGCAACAAGACCCGCTCCGCTATCGAATCCATCATGCAGGATGTCAAGACACTCGCACCTCACTACGAGACGCGCGTTGGCAAGCGGAAGTGGAACGAGAGGATGAAGAAGGGCGAGGCCGAGGAGTAAAAGTTCGCTCACGGTCAATTCCCGCCCCGAGATTGCCAGCACTACGTTCATCTTTGACGGTTTCTTCTCACTACGCACATGGACCGACTGCATGo to NCBI, select BLAST and paste this sequence in the window. Run a nucleotide BLAST vs all sequences (nr/nt) at, for the 3 levels provided: ‘somewhat similar’, ‘more dissimilar’ and ‘highly similar’. (You can just hit the Edit Search to do the re-runs. After each run write down the name of the bast hit and its e-value. What does an e-value tell you? What about the graphical interface . Also run at least one level search versus the est database. What is found in the est database in general and did you find any extra useful information? What are the best scores and E values you see? What do these values tell you? Look at the graphical representations and report what they tell you. Also look at the taxonomy report. What is the most distant relative shown?From a search that has a number of ‘hits’ use the ‘alignments’ tool to compare the different options. What would be best if you were trying to develop primers to amplify the equivalent sequence from a related species? WhyNow you can either Google for a free translation tool in the WEB that runs all 6 possible reading frames or use an NCBI Blast options to see if the sequence might encode a protein. Which option did you chose and why? Is the same organism identified in this case? ................
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