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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

bacteriaanalysissystemenglish.txt · Last modified: 2014/01/18 07:44 (external edit)