BLAST

• ​http://www.ncbi.nih.gov/BLAST/
• Debian 套件: ​blast2

【安裝】

   apt-get install blast2

【測試】

資料庫：

• ​ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/
• ​ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/blast-2.2.21-ia32-linux.tar.gz

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