Changes between Version 5 and Version 6 of biocluster/Clustal

Timestamp:

Sep 18, 2009, 11:35:26 AM (16 years ago)

Author:

wade

Comment:

--

biocluster/Clustal

@@ -33 +33 @@
 
 Your choice: 
-
     }}}
  1. 指令
@@ -48 +47 @@
 
 Enter the name of the sequence file : 
-
-    }}}
+    }}}
+ 1. 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: 
+    }}}
+ 1. 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: 
+    }}}
+ 1. 指令
+    {{{
+1
+    }}}
+    畫面
+    {{{
+Enter a name for the CLUSTAL output file  [kinase.aln]:
+    }}}
+ 1. 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]: 
+    }}}
+ 1. 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: 
+    }}}
+ 1. 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: 
+    }}}
+ 1. 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: 
+    }}}
+ 1. 指令：
+    {{{
+x
+    }}}
+    輸出檔案： kinase.aln 、 kinase.dnd 。