Results for "RepeatMasker"
Blogs
Common methods to discover tandem repeats
...n sequences. The tool uses a statistical algorithm to identify repeats based on their length, copy number, and overall composition. RepeatMasker: RepeatMasker is another software tool that...443 days ago
Bookmarks
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements,...e their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...2182 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The...on is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a few nece...1995 days ago
Top-level pages
Tools for Searching Repeats And Palindromic Sequences
...For more sophisticated repeat finding you will want to look at tools using Repbase for example: CENSOR CENSOR@GIRI CENSOR@EMBL-EBI RepeatMasker MUMmer (scan_for_match)...2231 days ago
Computational resources for TE discovery and TE detection
...www.girinst.org/ RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/ RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm RepeatMasker http://www.repeatmasker.org/ RepeatRunner http://ww...2293 days ago
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Wire posts
Bio-Scripts
Identify genome-wide synteny with LASTZ alignment
...Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_rice.fa AAChr1.txt RepeatMasker -pa 40 -nolow -norna -gff -xm...537 days ago
Perl script to find inverted repeats !
...s; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome..._seq(); my $seq = $seqobj->seq(); # run RepeatMasker my $rm = Bio::Tools::Run::Re...report = $rm->run($genome_file); # parse RepeatMasker output while (my $rm_result...445 days ago
Tags
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve correspond...Tags: perl, tool, conveniently, parse, RepeatMasker, output, files
2182 days ago
Steps to find all the repeats in the genome !
To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide: Install RepeatMasker: First, you need to install RepeatMasker on your system. You can download it from the RepeatMasker website[...Tags: Steps, Repeats, Genome, Perl, RepeatMasker
268 days ago
