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bacteriaanalysissystemenglish

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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.1188213316.txt.gz · Last modified: 2014/01/18 07:44 (external edit)