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bacteriaanalysissystemenglish [2007/08/27 11:15]
yves created
bacteriaanalysissystemenglish [2010/10/01 12:54]
ike
Line 12: Line 12:
 * Following is contents of BAS * Following is contents of BAS
  
-###############################################​############​ +  ​###############################################​ 
- +  # Bacteria Analysis System configuration file># 
-# Bacteria Analysis System configuration file># +  ###############################################​ 
- +  #$Id: BAS.conf,v 1.6 2001/09/09 11:53:20 s98982km Exp $ 
-###############################################​############​ +  #scripted by Koya Mori(mory@g-language.org) 
- +  #This is a configuration of Bacteria Analysis System 
- +    
-#$Id: BAS.conf,v 1.6 2001/09/09 11:53:20 s98982km Exp $ +  package G::​System::​BAS_conf;​  
- +    
-#scripted by Koya Mori(mory@g-language.org) +  use strict("​var"​);​  
- +    
-#This is a configuration of Bacteria Analysis System+  sub BAS{  
 +    my $methods;  
 +    
 +    $methods= <<'​CONF';​  
 +   
 +  #####################################​  
 +  #  G instances ​                     #  
 +  #####################################​  
 +   
 +  gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk  
 +      
 +  #####################################​  
 +  #  CAI                              #  
 +  #####################################​  
 +     
 +  >​cai ​           N 
 +     
 +  G-instance ​     $gb 
 +   
 +  -output ​                #[f or stdout] default:"​stdout"​ 
 +   
 +  -w_output ​              #[f or stdout] default:"​stdout"​ 
 +   
 +  -w_filename  
 +     .  
 +     .  
 +     .  
 +    (Abbreviation)  
 +     .  
 +     .  
 +     .
    
-package G::​System::​BAS_conf; ​ 
-  
-use strict("​var"​); ​ 
-  
-sub BAS{  
-my $methods; ​ 
-  
-$methods= <<'​CONF'; ​ 
- 
- 
-##################################### ​ 
- 
-#  G instances ​                     #  
- 
-##################################### ​ 
- 
-gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk ​ 
- 
-  
-##################################### ​ 
- 
-#  CAI                              #  
- 
-##################################### ​ 
- 
->​cai ​           N 
- 
-G-instance ​     $gb 
- 
--output ​                #[f or stdout] default:"​stdout"​ 
- 
--w_output ​              #[f or stdout] default:"​stdout"​ 
- 
--w_filename ​ 
-   ​. ​ 
-   ​. ​ 
-   ​. ​ 
-  (Abbreviation) ​ 
-   ​. ​ 
-   ​. ​ 
-   ​. ​ 
 We have 10 classes and 24 methods. We have 10 classes and 24 methods.
  
-CAI +  *CAI 
-cai +    *cai 
-Codon +  *Codon 
-codon_counter +    *codon_counter 
-amino_counter +    *amino_counter 
-codon_usage +    *codon_usage 
-Consensus +  *Consensus 
-base_counter +    *base_counter 
-base_information_content +    *base_information_content 
-base_z_value +    *base_z_value 
-base_entropy +    *base_entropy 
-base_relative_entropy +    *base_relative_entropy 
-base_individual_information_matrix +    *base_individual_information_matrix 
-GCskew +  *GCskew 
-view_cds +    *view_cds 
-find_ori_ter +    *find_ori_ter 
-gcskew +    *gcskew 
-genomicskew +    *genomicskew 
-cum_gcskew +    *cum_gcskew 
-gcwin +    *gcwin 
-Free Energy +  *Free Energy 
-foreach_RNAfold +    *foreach_RNAfold 
-Markov +  *Markov 
-over_lapping_finder +    *over_lapping_finder 
-Over Lapping Gene +  *Over Lapping Gene 
-over_lapping_finder +    *over_lapping_finder 
-Pat Search +  *Pat Search 
-palindrome +    *palindrome 
-Tandem Repeat +  *Tandem Repeat 
-foreach_tandem +    *foreach_tandem 
-graphical_LTR_search +    *graphical_LTR_search 
-Util +  *Util 
-seq2gif +    *seq2gif 
-genome_map+    *genome_map
  
 (2) choose an analysis data (2) choose an analysis data
  
 Default data is Escherichia_coli_K12. If you want to use another data, you have to change [gb1]. Also you can add a variable (ex.[mgen]). Default data is Escherichia_coli_K12. If you want to use another data, you have to change [gb1]. Also you can add a variable (ex.[mgen]).
 +
 * Before * Before
 +    ##################################### ​
 +    #  G instances ​                     # 
 +    ##################################### ​  
 +    gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk ​
  
  
-##################################### ​+* After 
 +    ​##################################### ​ 
 +    #  G instances ​                     # 
 +    #####################################​  
 +  gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk  
 +  mgen < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Mgen/​mgen.gbk ​   # add 
  
-#  G instances ​                     # +(3) Choose a method
  
-##################################### ​ 
  
 +This time we use [codon_usage](codon class),for example.
  
-gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk ​+・How to use [codon_usage]
  
 +1、First,​ turn [N] to [Y](this means switch on) and choose the analysis data at [G-instance]. If you want to put a output data into a file, change output option to [f]. You can find the file in [mgen]directory. And if you want to output a graph data, change output option to [g] (the graph is saved into [mgen/​graph]). Default option [show] means show all results including graph and standard output results automatically.
  
-* After 
  
-##################################### ​ 
  
-#  G instances ​                     #  
  
-##################################### ​+^-output |f |(put analysis data into a file) | 
 +^ |g |(output a graph analysis data) | 
 +^ |show |(show all analysis data automatically) | 
 +^-filename |free |(using[-output] option, you can named filename) |
  
  
-gb1 < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Ecoli/​ecoli.gbk ​ 
-mgen < /​pub/​dnadb/​ncbi/​genbank/​genomes/​bacteria/​Mgen/​mgen.gbk ​   # add  
-(3) Choose a method 
  
 +* Before
 +  >​codon_usage ​   N 
 +  G-instance ​     $gb 
 +  -CDSid ​
 +  -output ​        ​show ​   #[f or g or show] default:"​show" ​
 +  -filename ​
  
-This time we use [codon_usage](codon class),for example.+* After 
 +  >codon_usage ​   ​Y ​      # switch on  
 +  G-instance ​     gb1     # choose data  
 +  -CDSid  
 +  -output ​        ​g ​      #[f or g or showdefault:"​show"​  
 +  -filename ​
  
-How to use [codon_usage]+1. save the file.
  
-First, turn [N] to [Y](this means switch on) and choose the analysis data at [G-instance]If you want to put a output data into a file, change output option to [f]. You can find the file in [mgen]directoryAnd if you want to output a graph data, change output option to [g] (the graph is saved into [mgen/graph]). Default option [show] means show all results including graph and standard output results automatically.+2run the BAS 
 +          $./BAS 
  
--output f (put analysis data into a file+* Follwing is standard ​output ​results 
-g (output a graph analysis data+                 ​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​  
-show (show all analysis data automatically+      
--filename free (using [-output f] option, you can named filename)+                         ​G-language System  
 +      
 +                  Version: 1.0.0 gamma  
 +      
 +                  Copyright ​(C2001 G-language Project ​ 
 +                  ​Institute of Advanced Biosciences,​  
 +                  Keio University, JAPAN  
 +      
 +                     ​http://​www.g-language.org/​  
 +      
 +                 ​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​  
 +      
 +      Length of Sequence :    816394  
 +               A Content :    249211 ​(30.53%)  
 +               T Content :    240560 ​(29.47%)  
 +               G Content :    163703 ​(20.05% 
 +               C Content :    162920 (19.96%)  
 +                  Others :         0 (0.00%)  
 +              AT Content :    59.99%  
 +              GC Content :    40.01%  
 +                               .  
 +                               .  
 +                           ​(Abbreviation)  
 +                               .  
 +                               ​. ​
  
 +1. output the graph
 +  $ cd mgen/​graph ​
 +  $ gimp codon_table.gif ​
  
  
-* Before 
- 
->​codon_usage ​   N  
-G-instance ​     $gb  
--CDSid ​ 
--output ​        ​show ​   #[f or g or show] default:"​show" ​ 
--filename ​ 
-* After 
- 
->​codon_usage ​   Y       # switch on  
-G-instance ​     gb1     # choose data  
--CDSid ​ 
--output ​        ​g ​      #[f or g or show] default:"​show" ​ 
--filename ​ 
-save the file. 
-run the BAS 
-        $./​BAS ​ 
-* Follwing is standard output results 
-             ​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/ ​ 
-  
-                     ​G-language System ​ 
-  
-              Version: 1.0.0 gamma  
-  
-              Copyright (C) 2001 G-language Project ​ 
-              Institute of Advanced Biosciences, ​ 
-              Keio University, JAPAN  
-  
-                 ​http://​www.g-language.org/ ​ 
-  
-             ​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/​__/ ​ 
-  
-  Length of Sequence :    816394 ​ 
-           A Content :    249211 (30.53%) ​ 
-           T Content :    240560 (29.47%) ​ 
-           G Content :    163703 (20.05%) ​ 
-           C Content :    162920 (19.96%) ​ 
-              Others :         0 (0.00%) ​ 
-          AT Content :    59.99% ​ 
-          GC Content :    40.01% ​ 
-                           ​. ​ 
-                           ​. ​ 
-                       ​(Abbreviation) ​ 
-                           ​. ​ 
-                           ​. ​ 
-output the graph 
-        $cd mgen/​graph ​ 
-        $ gimp codon_table.gif ​ 
  
 +  *If you want to put analysis data into a file.
 +  *change output option to [f].
 +  *save the file
 +  *run the BAS.
 +  *output the file
  
 +  $ cd mgen
 +  $ emacs codon_usage.csv ​
  
-If you want to put analysis data into a file. 
-change output option to [f]. 
-save the file 
-run the BAS. 
-output the file 
-        $ cd mgen  
-        $ emacs codon_usage.csv ​ 
 * Following is standard output results * Following is standard output results
-/,​taa,​348,​0.725  +  ​/,​taa,​348,​0.725  
-/,​tag,​132,​0.275  +  /,​tag,​132,​0.275  
-A,​gca,​3759,​0.386  +  A,​gca,​3759,​0.386  
-A,​gcc,​730,​0.075  +  A,​gcc,​730,​0.075  
-A,​gcg,​462,​0.047  +  A,​gcg,​462,​0.047  
-A,​gct,​4799,​0.492  +  A,​gct,​4799,​0.492  
-C,​tgc,​295,​0.203  +  C,​tgc,​295,​0.203  
-C,​tgt,​1160,​0.797  +  C,​tgt,​1160,​0.797  
-D,​gac,​1196,​0.139  +  D,​gac,​1196,​0.139  
-D,​gat,​7388,​0.861  +  D,​gat,​7388,​0.861  
-    .  +      .  
-    .  +      .  
-    .  +      .  
- ​(Abbreviation)  +   ​(Abbreviation)  
-    .  +      .  
-    .  +      .  
-    +      
  
  
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 Written 10 September 2001 - Ryo Hattori Written 10 September 2001 - Ryo Hattori
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bacteriaanalysissystemenglish.txt · Last modified: 2014/01/18 07:44 (external edit)