Repeat search: Difference between revisions

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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 =
= Tandem repeats =
* satellites (spanning megabases of DNA, associated with heterochromatin)
* satellites (spanning megabases of DNA, associated with heterochromatin)
* minisatellites (repeat units in the range 6-100 bp, spanning hundreds of base-pairs)  
* 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).
* 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
* [http://www-is.biotoul.fr/ ISFinder]


= Software Packages =
= Software Packages =
* [http://mummer.sourceforge.net/manual/#repeat MUMer repeat-match] : does not classify the repeats
* [http://mummer.sourceforge.net/manual/#repeat MUMer repeat-match] :  
** does not classify the repeats
** works fine for small genomes
  ~/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
 
** does not work on large genomes
  split the genome in smaller pieces (10Mbp?)
  align them to one another:
  nucmer -l 20 -c 65  -g 90  -b 200  (default): takes too long
  nucmer -l 35 -c 2500 -g 100 
 
 
* [http://www.repeatmasker.org/RepeatModeler.html RepeatModeler]
* [http://www.repeatmasker.org/RepeatModeler.html RepeatModeler]
* [http://bix.ucsd.edu/repeatscout/ RepeatScout]
* [http://bix.ucsd.edu/repeatscout/ RepeatScout]
* [http://www.repeatmasker.org/ RepeatMasker] ; [http://www.girinst.org/server/RepBase RepBase] : mostly eukariotic genomes
* [http://www.repeatmasker.org/ RepeatMasker] ; [http://www.girinst.org/server/RepBase 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
* [http://minisatellites.u-psud.fr/GPMS/ Microorganisms Tandem Repeats Database (Online,FR)]
* [http://minisatellites.u-psud.fr/GPMS/ Microorganisms Tandem Repeats Database (Online,FR)]
* [http://crispr.u-psud.fr/Server/CRISPRfinder.php/ CRISPRfinder (Online,FR)]; [http://nar.oxfordjournals.org/cgi/content/full/gkm360v2 Article]
* [http://crispr.u-psud.fr/Server/CRISPRfinder.php/ CRISPRfinder (Online,FR)]; [http://nar.oxfordjournals.org/cgi/content/full/gkm360v2 Article]
* [http://tandem.bu.edu/trf/trf.html TRF]
* [http://tandem.bu.edu/trf/trf.html TRF]
= Articles =
* [http://www.nature.com/nrmicro/journal/v3/n9/full/nrmicro1233.html Mobile DNA in obligate intracellular bacteria]

Latest revision as of 18:25, 18 February 2010

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

  ~/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
    • does not work on large genomes
 split the genome in smaller pieces (10Mbp?)
 align them to one another:
 nucmer -l 20 -c 65   -g 90  -b 200  (default): takes too long
 nucmer -l 35 -c 2500 -g 100  


 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

Articles