How Do I Install and Use RepeatMasker

Why Did I Use RepeatMasker

Actually, RepeatMasker 'is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. So RepeatMasker take the sequences and compare them to a repeat library and finally replace the repeats in your query with 'N'or other non DNA bases.

Dependencies

  1. Unix system with perl
  2. TRF - Tandem Repeat Finder DOWNLOAD
  3. Sequence Search Engine  RMBlast DOWNLOAD
  4. Repeat Database DOWNLOAD : You need to open an account. Approval of account may take couple of days.
  5. RepeatMasker DOWNLOAD

Installation

  1. Unpack all softwares
  2. Copy TRF - Tandem Repeat Finder, RMBlast, makeblastdb and blastx exceutibles in RepeatMasker bin directory
  3. Tename Tandem Repeat Finder to trf
  4. In linus terminal, go to the bin directory of Repeatmasker and run
    perl ./configure
    
  5. This massage will appear in terminal
    RepeatMasker Configuration Program
    
    This program assists with the configuration of the
    RepeatMasker program.  The next set of screens will ask
    you to enter information pertaining to your system
    configuration.  At the end of the program your RepeatMasker
    installation will be ready to use.
    
    
    
    <PRESS ENTER TO CONTINUE>
    
    Now press enter
  6. This massage will appear in terminal
    **PERL PROGRAM**
    
      This is the full path to the Perl interpreter.
      e.g. /usr/local/bin/perl or enter "env" if you prefer to use
      the "/usr/bin/env perl" mechanism to locate perl.
    Enter path [ /usr/bin/perl ]:
    
    Now installer will search for PERL installation location. If it is different from above given path, then give the correct path for PERL to installer and press the enter.
  7. This massage will appear in terminal
    **REPEATMASKER INSTALLATION DIRECTORY**
    
      This is the path to the directory where
      the RepeatMasker program has been installed.
    
    Enter path [ /home/sanjay/Desktop/RepeatMasker ]:
    
    Now installer will search for RepeatMasker directory location. If it is different from above given path (I have extracted the downloaded RepeatMasker file on deskop), then give the correct path for RepeatMasker to installer and press the enter.
  8. This massage will appear in terminal
    **TRF PROGRAM**
    
      This is the full path to the TRF program.
     This is now used by RepeatMasker to mask simple repeats.
    
    Enter path [  ]:
    
    Now installer will search for Tandem Repeat Finder directory location. Since i have already copied the Tandem Repeat Finder in RepeatMasker directory therefore i will just copy the RepeatMasker directory path that is '/home/sanjay/Desktop/RepeatMasker' for me. If it is different from above given path , then give the correct path for Tandem Repeat Finder to installer and press the enter.

Journal Impact Factor 2013 - 2014 Download

Free Web Tools for miRNA Analysis

Easiet Way to Create A Heat Map In Excel