Repeat search: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| Line 1: | Line 1: | ||
= | = 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 = | |||
* [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 | ||
* [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 | ||
* [http://minisatellites.u-psud.fr/GPMS/ Microorganisms Tandem Repeats Database (Online,FR)] | |||
* [http://crispr.u-psud.fr/Server/CRISPRfinder.php/ CRISPRfinder (Online,FR)] | |||
Revision as of 11:16, 5 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
- Microorganisms Tandem Repeats Database (Online,FR)
- CRISPRfinder (Online,FR)