How to find repeat sequences on Genome in RepeatMasker
RepeatMasker how to find repeated sequences on the genome, for this problem, this article details the corresponding analysis and solution, hoping to help more small partners who want to solve this problem find a simpler and easier way.
RepeatMasker software is used to find repeated sequences in the genome. By default, it replaces the original base of the repeated sequence with N, thus achieving the purpose of labeling the repeated sequence. In addition, repeated sequences can also be marked by converting them to lowercase or removing them directly.
The software aligns the incoming DNA sequence with known repeats in the Dfam and Repbase databases to identify repeats in the incoming sequence. When comparing, support the following software
hmmer
cross_match
ABBlast/WUBlast
RMBlast
Choose one of them. Officially provided online services, the website is as follows
http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker
Input or upload FASTA format DNA sequence in Sequence;Search Engine selects alignment software, Speed/Sensitivity selects operation mode, the main difference between different modes lies in the difference of operation speed and sensitivity, DNA source selects reference species.
Of course, you can also download the software to run locally. The installation process is as follows
wget http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gztar xzvf RepeatMasker-open-4-0-7.tar.gzcd RepeatMaskerperl ./ configure
It is important to note that at least one of the above four comparison software needs to be installed. In addition, you need to install TRF software, link below
http://tandem.bu.edu/trf/trf.html
During installation, you need to specify the installation location of the comparison software and TRF software.
The basic usage of the software is as follows
RepeatMasker -pa 5 -small -species human chrM.fa
-pa specifies the number of threads, which only works if the input file is greater than 50Kb;-small converts repeated sequences to lowercase, and-species specifies the species referenced.
After the run is completed, multiple files will be generated. Files with the suffix masked are files marked with repeated sequences, and files with the suffix.out save repeated sequence interval information.
About RepeatMasker how to find repeated sequences on the genome to share the answer to the question here, I hope the above content can be of some help to everyone, if you still have a lot of doubts not solved, you can pay attention to the industry information channel to learn more related knowledge.
