wiki:biocluster/BLAST

BLAST

【安裝】

   apt-get install blast2

【測試】

資料庫:

  1. 指令:
    bl2seq -i nt.2655203 -j nt.3283410 -p blastn -o bl2seq.out
    
    輸出檔案:bl2seq.out
  2. 指令:
    formatdb -i nt.ests -p F -o T -n test.nt
    
    輸出檔案:
    • test.nt.nhr test.nt.nsd
    • test.nt.nin test.nt.nsi
    • test.nt.nnd test.nt.nsq
    • test.nt.nni formatdb.log
  3. 指令:
    fastacmd -d test.nt -s 5986
    
    畫面:
    CTTGAAGTTNTCGATAACAAATTTNTNATCCCAGAGAGAAAAGTGAACGAGGAGCCAATGTTTGCAGCGGANACGTTTAC
    TCGATCGTNGGGCGTGGAACAGTTATCACTGGAAAGCTTGAGAGAGGAATTTTNAAGAGAGGAGATAAGATTGAAATTNT
    TGGAGGAACAAAAGATGGAACCACTGTGAAATCAGTAATCTCTGGATTAGAATCCTTCCGTAAAACTGTCGATCAAGCCG
    AGCCTGGAGATCAATTGGNTGTGCTTCTTCGTGGTTTAGGNCCAAAAGATGTTCGTAGAGGATGTGTTTTACTTCCACAA
    GGNCACAAACATAAGGTCACTGATAAGGTTAAAGCTCAACTTTATGTGCTCAAAGAGAGC
    
  4. 指令:
    blastall -p blastn -d test.nt -i test.ests -e 0.1 -o blastall.out
    
    輸出檔案:blastall.out
    Query: 1   cttgaagttntcgataacaaatttntnatcccagagagaaaagtgaacgaggagccaatg 60
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct: 1   cttgaagttntcgataacaaatttntnatcccagagagaaaagtgaacgaggagccaatg 60
    
    
    Query: 61  tttgcagcgganacgtttactcgatcgtngggcgtggaacagttatcactggaaagcttg 120
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct: 61  tttgcagcgganacgtttactcgatcgtngggcgtggaacagttatcactggaaagcttg 120
    
    
    Query: 121 agagaggaattttnaagagaggagataagattgaaattnttggaggaacaaaagatggaa 180
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct: 121 agagaggaattttnaagagaggagataagattgaaattnttggaggaacaaaagatggaa 180
    
Last modified 15 years ago Last modified on Nov 11, 2009, 6:25:23 AM

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