Welcome to Integrated Bioinformatics Friday, 30 September

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Welcome toIntegrated BioinformaticsFriday, 30
September

• I. Intro to Scenario 3 Sequence alignment
• Bring up course web site
• Go to Scenario 3

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Gdansk, Poland
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MarborkCastle
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BlackDeath
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Scenario 3 Our Story
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Scenario 3 Our Story
You Our first defense at CDC
Outbreak
. . . Anthrax?

• Confirm agent

• Identify strain

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Scenario 3 Our Story
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Scenario 3 Our Story
DNA polymerase
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Scenario 3 Our Story
If DNA from bacterium with toxin gene
If DNA NOT from bacterium with toxin gene?
DNA polymerase
DNA polymerase
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Scenario 3 Our Story
DG47
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Scenario 3 Our Story
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Scenario 3 Our Story
DG47
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Scenario 3 Our Story
DG47
Maybe its not from the toxin gene??
(Try a different approach)
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Scenario 3 Our Story
DG47
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Never mind Blast, What's the real answer?(Do it
yourself)
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Scenario 3 Our Story
Compare nucleotide sequences by hand
DG47 vs lef
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Scenario 3 Our Story
Compare nucleotide sequences by hand
DG47      1  AATATTGACGCTTTACTACATCAGTCCATCGGAA
GTACGTTGTATAATAAAATATATCTG             

lef gene 1831 
AATATTGATGCTTTATTACATCAATCCATTGGAAGTACCTTGTACAATAA
AATTTATTTG   DG47       61  TATGAAAACATGAATATAAA
TAACTTAACAGCAACGTTAGGTGCCGATTTAGTAGATTCC
              
  lef gene 1891 
TATGAAAATATGAATATCAATAACCTTACAGCAACCCTAGGTGCGGATTT
AGTTGATTCC   DG47      121  ACAGATAATACAAAAATTAA
TCGAGGTATATTCAATGAGTTCAAAAAAAATTTCAAATAC   
           
lef gene 1951 
ACTGATAATACTAAAATTAATAGAGGTATTTTCAATGAATTCAAAAAAAA
TTTCAAATAT   DG47      181  AGTATTTCTA      
         lef gene 2011  AGTATTTCTA
89 identical!
Now let Blast do it by hand
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Scenario 3 Our Story
Compare nucleotide sequences by hand
DG47
lef gene
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Scenario 3 Our Story
Compare nucleotide sequences by hand
DG47
lef gene
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Scenario 3 Our Story
Why cant Blast figure outwhat you can plainly
see?
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Scenario 3 How does Blast work?

• Theory behind nucleotide vs nucleotide Blast

• Working BlastN program

• Theory behind protein-protein Blast

• How to get Blast to do what you want