bacteriaanalysissystemenglish

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]

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.

-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)

• 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 

1. save the file.

2. 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) 
                           . 
                           . 
  

1. 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