Repeat search

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Revision as of 18:48, 6 November 2008 by Dpuiu (talk | contribs)
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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

 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

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