Method 
find_tandem 
 
 
Class 
G::Seq::Tandem 
 
 
Function 
Finds tandem repeats from DNA sequences. 
 
Description 
Extracts tandem repeats from sequences.  By using this method, the simple repeat's pattern 
and its position can be extracted.  Extracted repeats are simple repeats; 
the user is able to chose the number of bases.  Yet it is best fit for the extraction of microsatellites 
of which are 3-15 bases long.  This method is only able to extract matches with patterns perfectly matching. 
 
 
Requirements 
 
  modules   
  SubOpt.pm 
 
  applications 
  none 
 
  data 
  none 
 
Parameters 
 
  essential 
  first     pointer   genome            G's instance 
 
  option 
  PatLength int       pattern_length    default=3 
  filename  string    file_name         default=tandem.csv 
  output    string    [stdout or f]     default=stdout 
 
Returns 
first     array    Repeat    Array of tandem repeats   
 
Usage 
(array Repeat)=&find_tandem(pointer GENOME,  -PatLength=>3, -output=>'stdout', -filename=>'tandem.csv'); 
 
Input file 
none 
 
Output file 
csv file in text format. 
 
References 
 
Comments 
 
Authors 
This method was written by Koya Mori(mory@g-language.org) at Institute for Advanced Biosciences Keio Univ.  
 
History 
Written 05 July   2001 - Koya Mori