安装RepeatMasker

简介

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

RepeatMasker 软件可以用来查找和屏蔽基因序列中的重复和低复杂度的序列。

在线查询

http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker

RepeatMasker Web Server screens DNA sequences in FASTA format against a library of repetitive elements and returns a masked query sequence ready for database searches. RepeatMasker also generates a table annotating the masked regions.

You can select a sequence file to process or paste the sequences(s) in FASTA format. But large sequences will be queued, and may take a while to process.

网页版可以输入fasta格式文件直接进行查询，但是对于比较的大文件不太方便，需要安装本地版本。

本地安装 1. Unix system with perl 5.8.0 or higher installed 2. Sequence Search Engine

RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross_Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system.

For Cross_Match go to http://www.phrap.org You will want to select "Phred/Phrap/Consed" as Cross_Match is part of the Phrap package.

For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/RMBlast.html

RMBlast的安装需要先安装BLAST+

For HMMER please download the v3.1b1 version here: http://hmmer.janelia.org/

For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ RepeatMasker 3.2.8 and above fully support both variants ]

NOTE: RepeatMasker open-3.2.9 or higher is required to use RMBlast.

这里以RMBlast的安装为例来做示范。

首先下载blast和RMBlast的最新安装包：

RMBlast:  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST

BLAST+:   ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST  

下载RMBlast 和 BLAST+的linux 版本，ncbi-blast-2.2.28+-x64-linux.tar.gz 和ncbi-rmblastn-2.2.28-x64-linux.tar.gz 解压之后将两个文件夹下的bin里的文件拷贝或者链接到同一个路径下，例如/mytmp/location/rmblast2.2.28。（其实主要是三个文件rmblastn，makeblastdb 和blastx） 

3. TRF - Tandem Repeat Finder, G. Benson et al.

   RepeatMasker was developed using TRF version 4.0.4， You can obtain a free copy athttp://tandem.bu.edu/trf/trf404.linux.download.html .

下载之后直接改名为 trf，复制到 /usr/local/bin 之类的地方，存放地址并不重要，只要在RepeatMasker编译的过程中准确引用其路径就可以。需要注意的是，trf 必须是可执行文件，所以需要改下属性，否则会导致RepeatMasker编译出问题。

chmod ugo+x trf （或者chmod a+x trf） 

4. Repeat Database

RepeatMasker will now work with custom libraries and with Dfam out of the box. Dfam is a database of profile HMM models of transposable elements ( only human at this point ) and is supported by RepeatMasker. For all other species we highly recommend obtaining the RepeatMasker version of RepBase. RepeatMasker searches are optimised to use this database and can produce higher quality annotations than can be acheived using the equivalent libraries with the -lib option.

To update the Dfam libraries contained in this release go to http://www.dfam.org.

To obtain RepBase for RepeatMasker go to http://www.girinst.org/server/RepBase/index.php

下载RepeatMasker的库需要注册Giri账号，可以申请免费账号，1-2个工作日Giri会给你注册的邮箱发密码邮件。得到账号之后，下载Repeatmasker版本的Repbase。

下载解压后，将RepeatMaskerLib.embl文件放在/mytmp/location/RepeatMasker/Libraries/ 文件夹下。 

5.RepeatMasker Installation 5.1 Download RepeatMasker

可以在 http://www.repeatmasker.org/RMDownload.html 获取Latest Released Version。

5.2 Unpack the distribution

Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /mytmp/location/ ). 

cp RepeatMasker-open-4-#-#.tar.gz /mytmp/location/

cd /mytmp/location/

gunzip RepeatMasker-open-4-#-#.tar.gz

tar xvf RepeatMasker-open-4-#-#.tar

5.3 Install RepeatMasker Libraries

(同4 解压Repbase到./RepeatMasker/Libraries)

Download the libraries from http://www.girinst.org and unpack in the RepeatMasker program directory. It is always best to use the most current.

5.4 Configure

cd /usr/local/RepeatMasker

perl ./configure

需要输入perl，RepeatMasker，trf绝对路径，最后需要选择比对软件及其绝对路径，并设置默认比对软件。

   出现下面的提示，就表示你成功安装了RepeatMasker。

Congratulations!  RepeatMasker is now ready to use.

The program is installed with a full version of the repeat library:

 DFAM Library Version = Dfam_1.2

 RMLibrary Version = 20130422

 Repbase Version = 20130422

Further documentation on the program may be found here:

/mytmp/location/RepeatMasker/repeatmasker.help

参考： 

http://www.repeatmasker.org/

http://azaleasays.com/2011/08/04/install-repeatmasker/

http://tandem.bu.edu/trf/trf404.linux.download.html

http://www.girinst.org/

http://www.repeatmasker.org/RMBlast.html

http://www.repeatmasker.org/webrepeatmaskerhelp.html