Repeat search: Difference between revisions
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* [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] | ||
Revision as of 16:45, 6 November 2008
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