Bioinformatics Tutorial

Exploring BLAST with Dino-DNA

"Jurassic Park" Dino-DNA Analysis

In 1990, Micheal Crichton published the book "Jurassic Park" about the resurrection of dinosaurs using the blood from the stomachs of insects which had been encased in tree sap, later turned into the mineral, amber.

At one point in the book, Dr. Henry Wu is asked to explain some of DNA techniques used in reconstructing the extinct dinosaur genomes. Dr. Wu describes the use of restriction enzymes and how the fragmented pieces of dino DNA can be spliced together with these enzymes. He also alludes to the fact that they don't have the entire genome but that they "fill in the gaps" with modern day frog DNA.

At one point during his discussion he points to a computer screen and remarks "Here you see the actual structure of a small fragment of dinosaur DNA."

>JurassicPark DinoDNA from the book Jurassic Park
gcgttgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatcgacgc
ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg
tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc
tgctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
agtaggacag gtgccggcag cgctctgggt cattttcggc gaggaccgct ttcgctggag
atcggcctgt cgcttgcggt attcggaatc ttgcacgccc tcgctcaagc cttcgtcact
ccaaacgttt cggcgagaag caggccatta tcgccggcat ggcggccgac gcgctgggct
ggcgttcgcg acgcgaggct ggatggcctt ccccattatg attcttctcg cttccggcgg
cccgcgttgc aggccatgct gtccaggcag gtagatgacg accatcaggg acagcttcaa
cggctcttac cagcctaact tcgatcactg gaccgctgat cgtcacggcg atttatgccg
caagtcagag gtggcgaaac ccgacaagga ctataaagat accaggcgtt tcccctggaa
gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg
ctttctcatt gctcacgctg taggtatctc agttcggtgt aggtcgttcg ctccaagctg
acgaaccccc cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca
acacgactta acgggttggc atggattgta ggcgccgccc tataccttgt ctgcctcccc
gcggtgcatg gagccgggcc acctcgacct gaatggaagc cggcggcacc tcgctaacgg
ccaagaattg gagccaatca attcttgcgg agaactgtga atgcgcaaac caacccttgg
ccatcgcgtc cgccatctcc agcagccgca cgcggcgcat ctcgggcagc gttgggtcct
gcgcatgatc gtgctagcct gtcgttgagg acccggctag gctggcgggg ttgccttact
atgaatcacc gatacgcgag cgaacgtgaa gcgactgctg ctgcaaaacg tctgcgacct
atgaatggtc ttcggtttcc gtgtttcgta aagtctggaa acgcggaagt cagcgccctg

In 1992, a young scientist, Dr. Mark Boguski, at the National Center for Biotechnology Information, NCBI, having read the book "Jurrasic Park"entered this sequence into a text editor and searched all of the known DNA sequences at the time. This collection of sequences make up a database refered to as GenBank. Mark wrote up his findings and submitted a manuscript to the journal BioTechniques, as a tongue-in-cheek joke. His manuscript was accepted and published. (Boguski, M.S. A Molecular Biologist Visits Jurassic Park. (1992) BioTechniques 12(5):668-669).

Any person reading "Jurrasic Park" who had access to a web browser could have performed this pure bioinformatics experiment and submitted an article for publication. You will reproduce Mark's experiment by using select, copy and paste to send this sequence for comparison against the GeneBank database just as Mark did in 1992.

Exercise 1

"The Lost World" Dino-DNA Analysis

Mark's published article was brought to Micheal 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 embeding a message in the protein translation of the DNA sequence which he submitted for use in the book.

Here is the sequence Mark gave Micheal 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

Dr. Mark Boguski is currently Senior Vice President, Research and Development, at Rosetta Inpharmatics in Kirkland, WA.