Method 
over_lapping_finder 
 
Class 
G::Seq::OverLapping; 
 
 
Function 
Finds overlapping genes. 
 
Description 
This method finds overlapping genes within the genome by referencing 
the CDS.  Even if the overlapping area is one base, this method extracts the data. 
 
The output data is shown in a upstream¡¡¢ª down stream order. 
When two genes are on the same chain, and facing the same direction, the situation in is "uni-directional." 
When upstream genes are overlapping on different chains, the situation is "end-on." 
When downtream genes are overlapping on different chains, the situation is "head-on." 
 
Requirements 
  applications   
SubOpt.pm 
 
applications 
none 
 
data 
none 
 
Parameters 
essential 
 
first     pointer   Genome      G's instance 
 
option 
output    string?  [stdout or f]    default=stdout 
filename  string  file_name         default=over_lapping.csv 
 
 
Returns 
none 
 
Usage 
&over_lapping_finder(pointer Genome, -output=>'stdout', -filename=>'over_lapping.csv'); 
 
Input file  
none 
 
Output file  
csv file in text format 
 
References 
none  
 
Comments 
none 
 
Authors 
This method was written by Koya Mori(mory@g-language.org) at Institute for Advanced Biosciences Keio Univ.  
 
 
History 
Written 22 July  2001 - Koya Mori