“Jurassic Park” Dino-DNA Analysis
Exercise 1 1. Go to the NCBI website (http://www.ncbi.nlm.nih.gov/). Click on “BLAST” and then “Nucleotide BLAST” (under Basic BLAST). Select, copy, and paste the sequence shown above into area labeled “Enter accession number, gi, or FASTA sequence”. Select the “Others (nr etc.)” option for databases but otherwise keep the default settings. At the bottom of the page, click the box for “Show results in a new window.” Then click the BLAST button at the bottom of the page. 2. Familiarize yourself with the results by following the various links to the alignments and GENBANK database entries. Follow the links are far as you can or as far as seems reasonable. 3. What are a few of the organisms that had sequences that best matched the dinosaur DNA sequence from “Jurassic Park?” Note that sequences with equal “E values” are equally similar to your query sequence. 4. Delete the Jurassic Park sequence from the Query field and replace it with about 100 random nucleotides. What kind of BLAST results do you get with random sequence? 5. From your results do you really believe what Dr. Wu is claiming? Did Michael Crichton just type random A, C, G, T letters or do you think he knew about GENBANK and borrowed some DNA? "The Lost World" Dino-DNA Analysis Mark's published article was brought to Michael Crichton's attention. In his second book, "The Lost World", Mr. Crichton used Mark as a consultant. Mark chose a DNA sequence from a living organism which is much more closely related to the dinosaurs. Mark also mixed in some frog, Xenopus, DNA just like Dr. Wu described to fill in the holes in their dino-genomes. However, Mark played a little trick on Mr. Crichton by embedding a message in the protein translation of the DNA sequence which he submitted for use in the book. Here is the sequence Mark gave Michael Crichton for the book "The Lost World": >LostWorld DinoDNA from the book The Lost World gaattccgga agcgagcaag agataagtcc tggcatcaga tacagttgga gataaggacg gacgtgtggc agctcccgca gaggattcac tggaagtgca ttacctatcc catgggagcc atggagttcg tggcgctggg ggggccggat gcgggctccc ccactccgtt ccctgatgaa gccggagcct tcctggggct gggggggggc gagaggacgg aggcgggggg gctgctggcc tcctaccccc cctcaggccg cgtgtccctg gtgccgtggg cagacacggg tactttgggg accccccagt gggtgccgcc cgccacccaa atggagcccc cccactacct ggagctgctg caaccccccc ggggcagccc cccccatccc tcctccgggc ccctactgcc actcagcagc gggcccccac cctgcgaggc ccgtgagtgc gtcatggcca ggaagaactg cggagcgacg gcaacgccgc tgtggcgccg ggacggcacc gggcattacc tgtgcaactg ggcctcagcc tgcgggctct accaccgcct caacggccag aaccgcccgc tcatccgccc caaaaagcgc ctgcgggtga gtaagcgcgc aggcacagtg tgcagccacg agcgtgaaaa ctgccagaca tccaccacca ctctgtggcg tcgcagcccc atgggggacc ccgtctgcaa caacattcac gcctgcggcc tctactacaa actgcaccaa gtgaaccgcc ccctcacgat gcgcaaagac ggaatccaaa cccgaaaccg caaagtttcc tccaagggta aaaagcggcg ccccccgggg gggggaaacc cctccgccac cgcgggaggg ggcgctccta tggggggagg gggggacccc tctatgcccc ccccgccgcc ccccccggcc gccgcccccc ctcaaagcga cgctctgtac gctctcggcc ccgtggtcct ttcgggccat tttctgccct ttggaaactc cggagggttt tttggggggg gggcgggggg ttacacggcc cccccggggc tgagcccgca gatttaaata ataactctga cgtgggcaag tgggccttgc tgagaagaca gtgtaacata ataatttgca cctcggcaat tgcagagggt cgatctccac tttggacaca acagggctac tcggtaggac cagataagca ctttgctccc tggactgaaa aagaaaggat ttatctgttt gcttcttgct gacaaatccc tgtgaaaggt aaaagtcgga cacagcaatc gattatttct cgcctgtgtg aaattactgt gaatattgta aatatatata tatatatata tatatctgta tagaacagcc tcggaggcgg catggaccca gcgtagatca tgctggattt gtactgccgg aattc Exercise 2 1. Select, copy, and paste the "Lost World" sequence shown above into the Nucleotide BLAST Search web form. Make sure the “others (nr etc.)” database is selected. 2. In the table of matches, follow the link to the GENBANK entry of the best match, this link is in the left most column labeled “Accession.” On that page find the ORGANISM keyword and click on the species link. This will bring up the species category of this organism. Do any of the terms imply a relationship to the dinosaurs? Click there to look at other descendents to the dinosaurs. What organism did Mark choose as being his living dinosaur? What is its common name? What is species for the second best match? What is its common name? 3. Go back to the main BLAST page. Click on “BLASTx.” This type of search translates the DNA sequence to six protein sequences (all three reading frames and forward or reverse) and searches the protein database. This search takes longer but is much informative about the relationship between the probe DNA sequence and the hits in the database. Select, copy, and paste the "Lost World" sequence into the Query Sequence form. Proteins use 20 letters instead of 4, this made it easier for Mark to create a hidden message. When the analysis is finished look at the best pairwise alignment by clicking on the score value in the right hand column or scroll down past the hit list to the first alignment – What was Mark's hidden message? Answer each of the six questions and copy and paste your answers into the Canvas submission box. “Jurassic Park” Dino-DNA Analysis 1. What are a few of the organisms that had sequences that best matched the dinosaur DNA sequence from “Jurassic Park?” Note that sequences with equal “E values” are equally similar to your query sequence. 2. What kind of BLAST results do you get with random sequence? 3. From your results do you really believe what Dr. Wu is claiming? Did Michael Crichton just type random A, C, G, T letters or do you think he knew about GENBANK and borrowed some DNA? “The Lost World” Dino-DNA Analysis 4. What organism did Dr. Mark Boguski choose as being his living dinosaur? What is its common name? Why did he choose this species? 5. What is species for the second best match? What is its common name? Why was this species selected? 6. What was Mark's hidden message in the amino acid sequence?