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BLAST Practice

BLAST Practice. http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome. BLAST homepage: Choose a program and/or a database. Enter Sequence. Choose Database. Limit by Entrez query: protease NOT hiv1[organism]

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BLAST Practice

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  1. BLAST Practice http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome

  2. BLAST homepage: Choose a program and/or a database

  3. Enter Sequence

  4. Choose Database

  5. Limit by Entrez query: protease NOT hiv1[organism] This will limit a BLAST search to all proteases, except those in HIV-1.

  6. 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?

  7. The sequence >DinoDNA from JURASSIC PARK p. 103 nt 1-1200 CCGGCTGGAAAATGCCTGCGGATATCCGCTTACAGCTGCGCGATAACACACTGATACTCAGTGATAACGG CGGCAGAAGCCTGTATTTTGAGCACCTGTTTCCCGGTGAGGACGGTTACAGCCGCAGCGAGTCACTCTGG CTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGCACTCTGGCAGGCGCTGCCGG AAGAACTCCGCTTAAGTCCGCATCGTTATCTGGCGACAAACAGTCCGCAGGGGCCGTGGTGGCTGCTCGG CTGGTGTGAGCGGGTGCCGGAAGCGGATGAGGTGCTGCCTGCGCCGCTGCCGCCGTACCGGGTACTGACC GGGCTGGTGGACCGCTTCGGGCGCACACAGACGTTCCACCGCGAAGCCGCCGGTGAATTCAGCGGCGAAA TCACCGGCGTGACGGATGGTGCCGGGCGTCACTTCCGGCTGGTACTGACCACGCAGGCGCAGCGGGCAGA AGAAGCCCGGCAGCAGGCCATTTCCGGCGGGACGGAACCGTCCGCTTTTCCTGATACCCTGCCGGGTTAC ACCGAATATGGCCGGGACAACGGCATCCGTCTGTCTGCCGTGTGGCTGACGCACGACCCGGAATACCCGG AGAATTTACCTGCCGCGCCGCTGGTGCGCTATGGCTGGACGCCGCGCGGCGAACTGGCGGTGGTGTATGA CCGTAGTGGCAAACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGT CACACGGGCCGGCCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGG CAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGA

  8. 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

  9. >DinoDNA from THE LOST WORLD p. 135 GAATTCCGGAAGCGAGCAAGAGATAAGTCCTGGCATCAGATACAGTTGGAGATAAGGACG GACGTGTGGCAGCTCCCGCAGAGGATTCACTGGAAGTGCATTACCTATCCCATGGGAGCC ATGGAGTTCGTGGCGCTGGGGGGGCCGGATGCGGGCTCCCCCACTCCGTTCCCTGATGAA GCCGGAGCCTTCCTGGGGCTGGGGGGGGGCGAGAGGACGGAGGCGGGGGGGCTGCTGGCC TCCTACCCCCCCTCAGGCCGCGTGTCCCTGGTGCCGTGGGCAGACACGGGTACTTTGGGG ACCCCCCAGTGGGTGCCGCCCGCCACCCAAATGGAGCCCCCCCACTACCTGGAGCTGCTG CAACCCCCCCGGGGCAGCCCCCCCCATCCCTCCTCCGGGCCCCTACTGCCACTCAGCAGC GGGCCCCCACCCTGCGAGGCCCGTGAGTGCGTCATGGCCAGGAAGAACTGCGGAGCGACG GCAACGCCGCTGTGGCGCCGGGACGGCACCGGGCATTACCTGTGCAACTGGGCCTCAGCC TGCGGGCTCTACCACCGCCTCAACGGCCAGAACCGCCCGCTCATCCGCCCCAAAAAGCGC CTGCTGGTGAGTAAGCGCGCAGGCACAGTGTGCAGCCACGAGCGTGAAAACTGCCAGACA TCCACCACCACTCTGTGGCGTCGCAGCCCCATGGGGGACCCCGTCTGCAACAACATTCAC GCCTGCGGCCTCTACTACAAACTGCACCAAGTGAACCGCCCCCTCACGATGCGCAAAGAC GGAATCCAAACCCGAAACCGCAAAGTTTCCTCCAAGGGTAAAAAGCGGCGCCCCCCGGGG GGGGGAAACCCCTCCGCCACCGCGGGAGGGGGCGCTCCTATGGGGGGAGGGGGGGACCCC TCTATGCCCCCCCCGCCGCCCCCCCCGGCCGCCGCCCCCCCTCAAAGCGACGCTCTGTAC GCTCTCGGCCCCGTGGTCCTTTCGGGCCATTTTCTGCCCTTTGGAAACTCCGGAGGGTTT TTTGGGGGGGGGGCGGGGGGTTACACGGCCCCCCCGGGGCTGAGCCCGCAGATTTAAATA ATAACTCTGACGTGGGCAAGTGGGCCTTGCTGAGAAGACAGTGTAACATAATAATTTGCA CCTCGGCAATTGCAGAGGGTCGATCTCCACTTTGGACACAACAGGGCTACTCGGTAGGAC CAGATAAGCACTTTGCTCCCTGGACTGAAAAAGAAAGGATTTATCTGTTTGCTTCTTGCT GACAAATCCCTGTGAAAGGTAAAAGTCGGACACAGCAATCGATTATTTCTCGCCTGTGTG AAATTACTGTGAATATTGTAAATATATATATATATATATATATATCTGTATAGAACAGCC TCGGAGGCGGCATGGACCCAGCGTAGATCATGCTGGATTTGTACTGCCGGAATTC

  10. Results What else can you see?

  11. Results What else can you see?

  12. 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.

  13. Fasta search Take the sequence below and run it against UniProt Knowledgebase http://www.ebi.ac.uk/Tools/sss/fasta/ MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMV MPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAG ASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLL TDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSI GFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTV GGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFAHWFPLFSGYTLNDTWAKIHFTIMFVG VNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSTMGSFISLTAVMLMIFMIWEAFASKREVAMVELTTT NIEWLHGCPPPYHTFEEPTYVIQK

  14. Results

  15. http://etest.vbi.vt.edu/etblast3/

  16. http://biosemantics.org/jane/

  17. Do it on JANE! (It takes too long on ETBLAST) It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to heaven, we were all going direct the other way - in short, the period was so far like the present period, that some of its noisiest authorities insisted on its being received, for good or for evil, in the superlative degree of comparison only.

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