Repeat search: Difference between revisions
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| Line 8: | Line 8: | ||
** up to 2Kbp | ** up to 2Kbp | ||
** no site specificity | ** no site specificity | ||
= Tandem repeats = | = Tandem repeats = | ||
| Line 14: | Line 13: | ||
* 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) = | = Insertion Elements(IS) = | ||
| Line 35: | Line 33: | ||
#elem min max mean median n50 sum | #elem min max mean median n50 sum | ||
Len 9055 4 35042 2205 890 4846 19966330 | 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] | |||
Revision as of 18:48, 6 November 2008
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
- 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