BLAST Practice

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BLAST Practice
http//blast.ncbi.nlm.nih.gov/Blast.cgi?CMDWebPA
GE_TYPEBlastHome
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BLAST homepage Choose a program and/or a database
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Enter Sequence
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Choose Database
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Limit by Entrez query protease NOT
hiv1organism This will limit a BLAST search to
all proteases, except those in HIV-1.
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Example

• Michael Crichton's fantasy about cloning
  dinosaurs, Jurassic Park, contains a putative
  dinosaur DNA sequence. Use Nucleotide BLAST
  against refseq_genomic to identify the source of
  this sequence.
• Select, copy, and paste it into the BLAST window.
  
• What organism is this dinosaur related to?

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The sequence

• gtDinoDNA from JURASSIC PARK p. 103 nt 1-1200
• CCGGCTGGAAAATGCCTGCGGATATCCGCTTACAGCTGCGCGATAACAC
  ACTGATACTCAGTGATAACGG
• CGGCAGAAGCCTGTATTTTGAGCACCTGTTTCCCGGTGAGGACGGTTACA
  GCCGCAGCGAGTCACTCTGG
• CTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGC
  ACTCTGGCAGGCGCTGCCGG
• AAGAACTCCGCTTAAGTCCGCATCGTTATCTGGCGACAAACAGTCCGCAG
  GGGCCGTGGTGGCTGCTCGG
• CTGGTGTGAGCGGGTGCCGGAAGCGGATGAGGTGCTGCCTGCGCCGCTGC
  CGCCGTACCGGGTACTGACC
• GGGCTGGTGGACCGCTTCGGGCGCACACAGACGTTCCACCGCGAAGCCGC
  CGGTGAATTCAGCGGCGAAA
• TCACCGGCGTGACGGATGGTGCCGGGCGTCACTTCCGGCTGGTACTGACC
  ACGCAGGCGCAGCGGGCAGA
• AGAAGCCCGGCAGCAGGCCATTTCCGGCGGGACGGAACCGTCCGCTTTTC
  CTGATACCCTGCCGGGTTAC
• ACCGAATATGGCCGGGACAACGGCATCCGTCTGTCTGCCGTGTGGCTGAC
  GCACGACCCGGAATACCCGG
• AGAATTTACCTGCCGCGCCGCTGGTGCGCTATGGCTGGACGCCGCGCGGC
  GAACTGGCGGTGGTGTATGA
• CCGTAGTGGCAAACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGG
  GCCGGATGGTGGCGCACCGT
• CACACGGGCCGGCCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGT
  GACAGAACAGCTAAACCCGG
• CAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACC
  GACAGCCTGAACCGCCGTGA

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• NCBI scientist Mark Boguski noticed this obvious
  "contaminant" and supplied Crichton with a better
  sequence, for the sequel book, The Lost World.
  Identify the most likely source of this sequence
  using translating BLAST (blastx) and nr database

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• gtDinoDNA from THE LOST WORLD p. 135
• GAATTCCGGAAGCGAGCAAGAGATAAGTCCTGGCATCAGATACAGTTGGA
  GATAAGGACG GACGTGTGGCAGCTCCCGCAGAGGATTCACTGGAAGTGC
  ATTACCTATCCCATGGGAGCC ATGGAGTTCGTGGCGCTGGGGGGGCCGG
  ATGCGGGCTCCCCCACTCCGTTCCCTGATGAA
  GCCGGAGCCTTCCTGGGGCTGGGGGGGGGCGAGAGGACGGAGGCGGGGGG
  GCTGCTGGCC TCCTACCCCCCCTCAGGCCGCGTGTCCCTGGTGCCGTGG
  GCAGACACGGGTACTTTGGGG ACCCCCCAGTGGGTGCCGCCCGCCACCC
  AAATGGAGCCCCCCCACTACCTGGAGCTGCTG
  CAACCCCCCCGGGGCAGCCCCCCCCATCCCTCCTCCGGGCCCCTACTGCC
  ACTCAGCAGC GGGCCCCCACCCTGCGAGGCCCGTGAGTGCGTCATGGCC
  AGGAAGAACTGCGGAGCGACG GCAACGCCGCTGTGGCGCCGGGACGGCA
  CCGGGCATTACCTGTGCAACTGGGCCTCAGCC
  TGCGGGCTCTACCACCGCCTCAACGGCCAGAACCGCCCGCTCATCCGCCC
  CAAAAAGCGC CTGCTGGTGAGTAAGCGCGCAGGCACAGTGTGCAGCCAC
  GAGCGTGAAAACTGCCAGACA TCCACCACCACTCTGTGGCGTCGCAGCC
  CCATGGGGGACCCCGTCTGCAACAACATTCAC
  GCCTGCGGCCTCTACTACAAACTGCACCAAGTGAACCGCCCCCTCACGAT
  GCGCAAAGAC GGAATCCAAACCCGAAACCGCAAAGTTTCCTCCAAGGGT
  AAAAAGCGGCGCCCCCCGGGG GGGGGAAACCCCTCCGCCACCGCGGGAG
  GGGGCGCTCCTATGGGGGGAGGGGGGGACCCC
  TCTATGCCCCCCCCGCCGCCCCCCCCGGCCGCCGCCCCCCCTCAAAGCGA
  CGCTCTGTAC GCTCTCGGCCCCGTGGTCCTTTCGGGCCATTTTCTGCCC
  TTTGGAAACTCCGGAGGGTTT TTTGGGGGGGGGGCGGGGGGTTACACGG
  CCCCCCCGGGGCTGAGCCCGCAGATTTAAATA
  ATAACTCTGACGTGGGCAAGTGGGCCTTGCTGAGAAGACAGTGTAACATA
  ATAATTTGCA CCTCGGCAATTGCAGAGGGTCGATCTCCACTTTGGACAC
  AACAGGGCTACTCGGTAGGAC CAGATAAGCACTTTGCTCCCTGGACTGA
  AAAAGAAAGGATTTATCTGTTTGCTTCTTGCT
  GACAAATCCCTGTGAAAGGTAAAAGTCGGACACAGCAATCGATTATTTCT
  CGCCTGTGTG AAATTACTGTGAATATTGTAAATATATATATATATATAT
  ATATATCTGTATAGAACAGCC TCGGAGGCGGCATGGACCCAGCGTAGAT
  CATGCTGGATTTGTACTGCCGGAATTC

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Results
What else can you see?
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Results
What else can you see?
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If the sequence is already in NCBI

• BLink (BLAST Link) is a tool that displays the
  pre-computed results of BLAST searches that have
  been completed for every protein sequence in the
  Entrez Proteins data domain.