BLAST Practice

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BLAST Practice
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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
• GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACA
  AAAATCGACGC GGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCG
  TTTCCCCCTGGAAGCTCCCTCG TGTTCCGACCCTGCCGCTTACCGGATA
  CCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGC
  TGCTCACGCTGTACCTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCT
  GGGCTGTGTG CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATC
  GTCTTGAGTCCAACCCGGTAA AGTAGGACAGGTGCCGGCAGCGCTCTGG
  GTCATTTTCGGCGAGGACCGCTTTCGCTGGAG
  ATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGC
  CTTCGTCACT CCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCA
  TGGCGGCCGACGCGCTGGGCT GGCGTTCGCGACGCGAGGCTGGATGGCC
  TTCCCCATTATGATTCTTCTCGCTTCCGGCGG
  CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGG
  ACAGCTTCAA CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGA
  TCGTCACGGCGATTTATGCCG CACATGGACGCGTTGCTGGCGTTTTTCC
  ATAGGCTCCGCCCCCCTGACGAGCATCACAAA
  CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTT
  CCCCCTGGAA GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCT
  GTCCGCCTTTCTCCCTTCGGG CTTTCTCAATGCTCACGCTGTAGGTATC
  TCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTG
  ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGT
  CTTGAGTCCA ACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCC
  CTATACCTTGTCTGCCTCCCC GCGGTGCATGGAGCCGGGCCACCTCGAC
  CTGAATGGAAGCCGGCGGCACCTCGCTAACGG
  CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAAC
  CAACCCTTGG CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCA
  TCTCGGGCAGCGTTGGGTCCT

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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.

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http//www.ncbi.nlm.nih.gov/Class/minicourses/blas
tex2.html
Work on the questions that are marked with
Standard protein-protein BLAST blastp Search
for short nearly exact matches Nucleotide query -
Protein db blastx Human Genome