Method 
mask_repeat 
 
Classpackage  
G::Tools::Mapping; 
 
 
Function 
Applies RepeatMasker on sequences 
 
Description 
This method uses RepeatMasker, and masks the repeative sequences of a given sequence by N. 
 
Transposonsˇ˘simple repeatsˇ˘and GC complexities are masked. 
For transposons, the database to be referenced can be specified.   
Be aware that it takes a lot of time to run this method.   
This program will not work if RepeatMasker is not installed. 
 
 
Requirements 
SubOpt.pm 
 
applications 
Repeat Masker 
 
data 
none 
 
Parameters 
essential 
 
first     string   cdna_file        filename of cdna 
second    string   query_directory  the pass of the query directory  
 
 
option 
first     string    -lib    the library for RepeatMasker    default=human 
 
Returns 
none 
 
Usage 
&mask_repeat(string cdna_file, string query_directory, -lib=>'human'); 
 
Input file  
none 
 
 
Output file  
none 
 
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 8/17   - Koya Mori