BAS(Bacteria Analysis System) Tutorial

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.

        $ emacs BAS.conf 

########################################################### 
#  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

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]).

##################################### 
#  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.

* 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 

             __/__/__/__/__/__/__/__/__/__/__/__/__/ 
 
                     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 

/,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