wiki:biocluster/Clustal

Version 7 (modified by wade, 15 years ago) (diff)

--

http://www.clustal.org/

以 ClustalW 為主。

【安裝】

   wget http://www.clustal.org/download/current/clustalw-2.0.12-linux-i686-libcppstatic.tar.gz
   tar zxvf clustalw-2.0.12-linux-i686-libcppstatic.tar.gz

【測試】

  1. 指令:
    clustalw2
    
    畫面:
     **************************************************************
     ******** CLUSTAL 2.0.11 Multiple Sequence Alignments  ********
     **************************************************************
    
    
         1. Sequence Input From Disc
         2. Multiple Alignments
         3. Profile / Structure Alignments
         4. Phylogenetic trees
    
         S. Execute a system command
         H. HELP
         X. EXIT (leave program)
    
    
    Your choice: 
    
  2. 指令
    1
    
    畫面
    Sequences should all be in 1 file.
    
    7 formats accepted: 
    NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF,                  RSF.
    
    
    Enter the name of the sequence file : 
    
  3. 指令
    kinase.tfa
    
    畫面
    Sequence format is Pearson
    Sequences assumed to be PROTEIN
    
    
    Sequence 1: KAPA_MOUSE   350 aa
    Sequence 2: KDCA_DROME   354 aa
    Sequence 3: ARK1_HUMAN   689 aa
    Sequence 4: KGP2_DROME  1088 aa
    Sequence 5: YPK2_YEAST   677 aa
    Sequence 6: VIP_MELGA    444 aa
    Sequence 7: K6A3_HUMAN   740 aa
    Sequence 8: DMK_HUMAN    639 aa
    Sequence 9: KPBG_RABIT   386 aa
    Sequence 10: KCC1_YEAST   446 aa
    Sequence 11: PIM1_HUMAN   313 aa
    Sequence 12: KRAF_DROME   781 aa
    Sequence 13: TRKB_HUMAN   822 aa
    Sequence 14: INSR_HUMAN  1382 aa
    Sequence 15: KPRO_MAIZE   817 aa
    Sequence 16: DAF1_CAEEL   669 aa
    
    
    
     **************************************************************
     ******** CLUSTAL 2.0.11 Multiple Sequence Alignments  ********
     **************************************************************
    
    
         1. Sequence Input From Disc
         2. Multiple Alignments
         3. Profile / Structure Alignments
         4. Phylogenetic trees
    
         S. Execute a system command
         H. HELP
         X. EXIT (leave program)
    
    
    Your choice: 
    
  4. 指令
    2
    
    畫面
    ****** MULTIPLE ALIGNMENT MENU ******
    
    
        1.  Do complete multiple alignment now Slow/Accurate
        2.  Produce guide tree file only
        3.  Do alignment using old guide tree file
    
        4.  Toggle Slow/Fast pairwise alignments = SLOW
    
        5.  Pairwise alignment parameters
        6.  Multiple alignment parameters
    
        7.  Reset gaps before alignment? = OFF
        8.  Toggle screen display          = ON
        9.  Output format options
        I. Iteration = NONE
    
        S.  Execute a system command
        H.  HELP
        or press [RETURN] to go back to main menu
    
    
    Your choice: 
    
  5. 指令
    1
    
    畫面
    Enter a name for the CLUSTAL output file  [kinase.aln]:
    
  6. 指令
    按 Enter 
    
    畫面
    Start of Pairwise alignments
    Aligning...
    
    Sequences (1:2) Aligned. Score:  45
    Sequences (1:3) Aligned. Score:  26
    Sequences (1:4) Aligned. Score:  36
    ............
    Sequences (14:16) Aligned. Score:  11
    Sequences (15:16) Aligned. Score:  11
    Enter name for new GUIDE TREE           file   [kinase.dnd]: 
    
  7. 指令
    按 Enter 
    
    畫面
    There are 15 groups
    Start of Multiple Alignment
    
    Aligning...
    Group 1:                     Delayed
    Group 2: Sequences:   2      Score:5585
    Group 3: Sequences:   2      Score:6757
    Group 4: Sequences:   4      Score:4840
    Group 5: Sequences:   5      Score:4243
    Group 6:                     Delayed
    Group 7:                     Delayed
    Group 8:                     Delayed
    Group 9:                     Delayed
    Group 10:                     Delayed
    Group 11:                     Delayed
    Group 12:                     Delayed
    Group 13:                     Delayed
    Group 14:                     Delayed
    Group 15:                     Delayed
    Alignment Score -1627
    
    
    
    Consensus length = 1608 
    
    CLUSTAL-Alignment file created  [kinase.aln]
    
    
    CLUSTAL 2.0.11 multiple sequence alignment
    
    
    KAPA_MOUSE      ------------------------------------------------------------
    KDCA_DROME      ------------------------------------------------------------
    YPK2_YEAST      ------------------------------------------------------------
    VIP_MELGA       ------------------------------------------------------------
    K6A3_HUMAN      ------------------------------------------------------------
    PIM1_HUMAN      ------------------------------------------------------------
    KGP2_DROME      MRFCFDRLCFATKRPAQNSNSNAPHSSTTVDAPPRPADVDVATVPVATTAPPPQQPVSNL
    DMK_HUMAN       ------------------------------------------------------------
    KPBG_RABIT      ------------------------------------------------------------
    KCC1_YEAST      ------------------------------------------------------------
    ARK1_HUMAN      ------------------------------------------------------------
    INSR_HUMAN      ------------------------MGTGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCP
    TRKB_HUMAN      ------------------------------------------------------------
    KPRO_MAIZE      ------------------------------------------------------------
    KRAF_DROME      ------------------------------------------------------------
    DAF1_CAEEL      ------------------------------------------------------------
                                                                                
    
    KAPA_MOUSE      ------------------------------------------------------------
    
    Press [RETURN] to continue or  X  to stop: 
    
  8. 指令
    x
    
    畫面
    ****** MULTIPLE ALIGNMENT MENU ******
    
    
        1.  Do complete multiple alignment now Slow/Accurate
        2.  Produce guide tree file only
        3.  Do alignment using old guide tree file
    
        4.  Toggle Slow/Fast pairwise alignments = SLOW
    
        5.  Pairwise alignment parameters
        6.  Multiple alignment parameters
    
        7.  Reset gaps before alignment? = OFF
        8.  Toggle screen display          = ON
        9.  Output format options
        I. Iteration = NONE
    
        S.  Execute a system command
        H.  HELP
        or press [RETURN] to go back to main menu
    
    
    Your choice: 
    
  9. 指令
    按 Enter
    
    畫面
     **************************************************************
     ******** CLUSTAL 2.0.11 Multiple Sequence Alignments  ********
     **************************************************************
    
    
         1. Sequence Input From Disc
         2. Multiple Alignments
         3. Profile / Structure Alignments
         4. Phylogenetic trees
    
         S. Execute a system command
         H. HELP
         X. EXIT (leave program)
    
    
    Your choice: 
    
  10. 指令:
    x
    
    輸出檔案: kinase.aln 、 kinase.dnd 。

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