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bacteriaanalysissystemenglish [2007/08/27 11:15]
yves created
bacteriaanalysissystemenglish [2014/01/18 07:44]
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-====== Overview ====== 
- 
- 
-BAS is a collection of perl modules that facilitate the development of perl scripts for bio-informatics applications. This document is a tutorial for BAS. In order to take advantage of BAS, all you have to do is change a few setup. 
- 
-====== How to change a setup ====== 
- 
- 
-Let's take an example. 
-(1) Open the configuration file[BAS.conf] 
-        $ emacs BAS.conf ​ 
-* Following is contents of BAS 
- 
-###########################################################​ 
- 
-# 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 
-  
-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. 
- 
-CAI 
-cai 
-Codon 
-codon_counter 
-amino_counter 
-codon_usage 
-Consensus 
-base_counter 
-base_information_content 
-base_z_value 
-base_entropy 
-base_relative_entropy 
-base_individual_information_matrix 
-GCskew 
-view_cds 
-find_ori_ter 
-gcskew 
-genomicskew 
-cum_gcskew 
-gcwin 
-Free Energy 
-foreach_RNAfold 
-Markov 
-over_lapping_finder 
-Over Lapping Gene 
-over_lapping_finder 
-Pat Search 
-palindrome 
-Tandem Repeat 
-foreach_tandem 
-graphical_LTR_search 
-Util 
-seq2gif 
-genome_map 
- 
-(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]). 
-* 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  
-(3) Choose a method 
- 
- 
-This time we use [codon_usage](codon class),for example. 
- 
-How to use [codon_usage] 
- 
-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. 
- 
--output f (put analysis data into a file) 
-g (output a graph analysis data) 
-show (show all analysis data automatically) 
--filename free (using [-output f] option, you can named filename) 
- 
- 
- 
-* 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 ​ 
-* Following is standard output results 
-/,​taa,​348,​0.725 ​ 
-/,​tag,​132,​0.275 ​ 
-A,​gca,​3759,​0.386 ​ 
-A,​gcc,​730,​0.075 ​ 
-A,​gcg,​462,​0.047 ​ 
-A,​gct,​4799,​0.492 ​ 
-C,​tgc,​295,​0.203 ​ 
-C,​tgt,​1160,​0.797 ​ 
-D,​gac,​1196,​0.139 ​ 
-D,​gat,​7388,​0.861 ​ 
-    .  
-    .  
-    .  
- ​(Abbreviation) ​ 
-    .  
-    .  
-    .  
- 
- 
-====== Notes ====== 
- 
- 
-There is difference between [Essential] and [option]. [option] has [-] before option name(ex. -CDSid ), but [Essential] hasn'​t. You must to put variable into [Essential],​ but [option] is not. 
->​codon_usage ​   Y  
-G-instance ​     gb1                                         ## ​ Essential ​ ##  
--CDSid ​                                                      # ​ option ​ #  
--output ​        ​f ​      #[f or g or show] default:"​show" ​    # ​ option ​ #  
--filename ​                                                   #  option ​ #  
- 
- 
- 
- 
- 
-Written 10 September 2001 - Ryo Hattori 
  
bacteriaanalysissystemenglish.txt ยท Last modified: 2014/01/18 07:44 (external edit)