Repeat search

Tandem repeats

• satellites (spanning megabases of DNA, associated with heterochromatin)
• minisatellites (repeat units in the range 6-100 bp, spanning hundreds of base-pairs)
• microsatellites (repeat units in the range 1-5 bp, spanning a few tens of nucleotides).

Software Packages

• MUMer repeat-match : does not classify the repeats
• RepeatModeler
• RepeatScout
• RepeatMasker ; RepBase : mostly eukariotic genomes

 Library:
   $ ls /fs/szdevel/dpuiu/RepeatMasker/Libraries/RepeatMaskerLib.embl 
 
   $ ~/bin//readseq.sh -f Fasta -o RepeatMaskerLib.fasta RepeatMaskerLib.embl
 
   $ infoseq RepeatMaskerLib.fasta | getSummary.pl -c 1 -t Len
             #elem   min     max     mean    median  n50     sum
     Len     9055    4       35042   2205    890     4846    19966330

• Microorganisms Tandem Repeats Database (Online,FR)
• CRISPRfinder (Online,FR); Article
• TRF