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 = | ||
Revision as of 18:47, 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