RepeatModeler安装及使用

Posted 2021-03-08 zhanmaomao

如果进行重复序列的预测，则使用RepeatModeler，可自身比对进行查找

 

• 安装

（1）下载地址：http://www.repeatmasker.org/RepeatModeler/

（2）RepeatModeler安装之前需要安装以下软件

• perl
• RECON - De Novo Repeat Finder;  鉴定重复家族
• RepeatScout - De Novo Repeat Finder; 从基因组中鉴定重复序家族序列
• TRF - Tandem Repeat Finder
• RMBlast - A modified version of NCBI Blast for use with RepeatMasker and RepeatModeler.或者
• ABBlast - Sequence Search Engine    任一一款搜索引擎
• RepeatMasker & Libraries

（2.1）各个软件详细安装方法

• RECON

1 #下载后
2 tar -zxf RECON-1.08.tar.gz
3 cd RECON-1.08/src
4 make
5 make install
6 #给recon.pl脚本中添加路径，第三行
7 $path = "*/RECON-1.08/bin"

• RepeatScout

1 #下载后
2 tar -zxf RepeatScout-1.0.6.tar.gz
3 cd RepeatScout-1.0.6
4 make
5 ##会生成build_lmer_table， RepeatScout-###两个程序

• TRF

 1 #选择Linux command line 64-bit ，下载后，直接使用，不需要解压缩 

• RMBlast

#下载后
tar -zxf rmblast-2.10.0+-x64-linux.tar.gz
#即可

• RepeatMasker（事先必须安装TRF，RMblast）

 1 #下载后
 2 tar -zxf RepeatMasker-4.1.0.tar.gz
 3 cd RepeatMasker
 4 chmod -R 755 *
 5 ./configure. 执行后一步一步来，输入需要的路径
 6 
 7 #首先是perl环境，默认自动检测，或者手动更改perl主程序路径后回车继续
 8 #然后是TRF， 输入包含TRF的路径
 9 #序列搜索引擎，刚才安装了RMblast，先选择RMblast，然后回车，然后选择5 done
10 #提示 完成安装，将RepeatMasker设置到环境变量即可

（3）安装RepeatModeler

1 #下载后
2 tar. -zxf RepeatModeler-2.0.1.tar.gz
3 cd RepeatModeler-2.0.1
4 chmod -R 755 *
5 perl ./configure  根据提示，一步一步来，和上面repeatmasker类似

• 使用

（1）RepeatModeler 预测基因组重复序列，为下一步的RepeatMasker建立重复序列数据库

 1 #建库，利用rice 一个实例fasta文件
 2 BuildDatablase –name ricedb –engine ncbi  rice.sample.2.fa
 3 
 4 #参数说明
 5 -name <database name>
 6         The name of the database to create.
 7 -engine <engine name>
 8         The name of the search engine we are using. I.e abblast/wublast or rmblast.
 9 -dir <directory>
10         The name of a directory containing fasta files to be processed. The
11         files are recognized by their suffix. Only *.fa and *.fasta files
12         are processed.
13 -batch <file>
14         The name of a file which contains the names of fasta files to
15         process. The files names are listed one per line and should be fully
16         qualified.
17 
18 RepeatModeler -database ricedb  -pa 5
19 
20 #参数说明
21 -database
22         The name of the sequence database to run an analysis on. This is the
23         name that was provided to the BuildDatabase script using the "-name"
24         option.
25 -pa #
26         Specify the number of parallel search jobs to run. RMBlast jobs will
27         use 4 cores each and ABBlast jobs will use a single core each. i.e.
28         on a machine with 12 cores and running with RMBlast you would use
29         -pa 3 to fully utilize the machine.
30 -recoverDir <Previous Output Directory>
31         If a run fails in the middle of processing, it may be possible
32         recover some results and continue where the previous run left off.
33         Simply supply the output directory where the results of the failed
34         run were saved and the program will attempt to recover and continue
35         the run.

（1.1）RepeatModeler结果文件

• consensi.fa：自身比对找到的一致性序列
• consensi.fa.classified：重复序列分类结果，“#”后面的字符串是分类结果
• consensi.fa.masked：屏蔽后的序列，不太使用

（2）RepeatMasker；屏蔽DNA序列中转座子或者低复杂度重复序列，输出的序列把已知的重复序列都屏蔽成N或X，并给出相应的位置和统计信息

 1 #将上一步的结果文件（自动生成，以“RM”开头）里面的consensi.fa.classified为libirary，对参考序列进行序列屏蔽
 2 #运行
 3 RepeatMasker -nolow  -e ncbi -pa 5 -norna -dir ./  -lib consensi.fa.classified rice.sample.fa
 4 
 5 #重要参数
 6 -nolow. (不屏蔽低复杂序列，担心屏蔽后使得基因结构受到影响)
 7         Does not mask low_complexity DNA or simple repeats
 8 -lib [filename] 自己制定的重复序列库
 9         Allows use of a custom library (e.g. from another species)
10  -e(ngine) [crossmatch|wublast|abblast|ncbi|rmblast|hmmer]
11         Use an alternate search engine to the default.
12 -pa(rallel) [number]
13         The number of sequence batch jobs [50kb minimum] to run in parallel.
14 -norna
15         Does not mask small RNA (pseudo) genes
16 -dir [directory name] 输出文件位置
17         Writes output to this directory (default is query file directory,
18         "-dir ." will write to current directory).
19 -gff
20         Creates an additional Gene Feature Finding format output

（2.1）RepeatMasker输出结果

• *.out：重复序列详细比对结果
• *.masked：屏蔽后的序列
• *.tbl：重复序列统计文件
• *.cat：和out差不多

最后将out文件可转为GFF文件，即完成基因组重复序列的鉴定。