Repeat search

Mobile elements

• plasmids
• bacteriophages:
  • up to 20% of the genome
  • most common transporters of virulence genes in bacteria
  • have site specificity
• transposable elements
  • up to 2Kbp
  • no site specificity

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).

Insertion Elements(IS)

• 0.7-2.5K bp
• small, genetically compact (1-2 ORFs) : transposase and/or reverse transcriptase
• end in short terminal inverted repeat sequences (IR) 10-40bp
• ISFinder

Software Packages

• MUMer repeat-match : does not classify the repeats

  ~/bin/RepeatSearch.amos prefix
 ...
 10: $(BINPATH)/repeat-match -n $(REPEATLEN) $(PREFIX).fasta | $(SCRIPTPATH)/repeat-match2gff.pl > $(REPEATS).gff
 20: $(SCRIPTPATH)/extractfromfastagff.pl $(PREFIX).fasta $(REPEATS).gff > $(REPEATS).fasta

 30: $(BINPATH)/nucmer -maxmatch $(REPEATS).fasta $(REPEATS).fasta -p $(REPEATS)
 40: $(BINPATH)/show-coords  -c -l  -r -o -H $(REPEATS).delta  | awk '{print $18,$19}' | ~/bin/cluster.pl > $(REPEATS).cluster
 50: $(SCRIPTPATH)/extractfromfastanames.pl -f $(REPEATS).cluster < $(REPEATS).fasta > $(REPEATS).cluster.fasta

• 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

Articles

• Mobile DNA in obligate intracellular bacteria