Repeat search - Revision history

Dpuiu: /* Software Packages */

2010-02-18T18:25:35Z

Software Packages

← Older revision		Revision as of 18:25, 18 February 2010
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	= 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		~/bin/RepeatSearch.amos prefix
	...		...
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	40: $(BINPATH)/show-coords -c -l -r -o -H $(REPEATS).delta \| awk '{print $18,$19}' \| ~/bin/cluster.pl > $(REPEATS).cluster		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		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]

Dpuiu: /* Software Packages */

2010-01-24T19:29:57Z

Software Packages

← Older revision		Revision as of 19:29, 24 January 2010
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	10: $(BINPATH)/repeat-match -n $(REPEATLEN) $(PREFIX).fasta \| $(SCRIPTPATH)/repeat-match2gff.pl > $(REPEATS).gff		10: $(BINPATH)/repeat-match -n $(REPEATLEN) $(PREFIX).fasta \| $(SCRIPTPATH)/repeat-match2gff.pl > $(REPEATS).gff
	20: $(SCRIPTPATH)/extractfromfastagff.pl $(PREFIX).fasta $(REPEATS).gff > $(REPEATS).fasta		20: $(SCRIPTPATH)/extractfromfastagff.pl $(PREFIX).fasta $(REPEATS).gff > $(REPEATS).fasta

	30: $(BINPATH)/nucmer -maxmatch $(REPEATS).fasta $(REPEATS).fasta -p $(REPEATS)		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		40: $(BINPATH)/show-coords -c -l -r -o -H $(REPEATS).delta \| awk '{print $18,$19}' \| ~/bin/cluster.pl > $(REPEATS).cluster

Dpuiu: /* Software Packages */

2010-01-14T16:08:25Z

Software Packages

← Older revision		Revision as of 16:08, 14 January 2010
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	= 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
			~/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

	* [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]

Dpuiu at 18:48, 6 November 2008

2008-11-06T18:48:33Z

← Older revision		Revision as of 18:48, 6 November 2008
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	** up to 2Kbp		** up to 2Kbp
	** no site specificity		** no site specificity


	= Tandem repeats =		= Tandem repeats =
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	* 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) =
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	#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]

Dpuiu: /* Tandem repeats */

2008-11-06T18:47:34Z

Tandem repeats

@@ 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 =

Dpuiu: /* Software Packages */

2008-11-06T16:45:55Z

Software Packages

← Older revision		Revision as of 16:45, 6 November 2008
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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]

Dpuiu: /* Software Packages */

2008-11-05T20:19:02Z

Software Packages

← Older revision		Revision as of 20:19, 5 November 2008
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	* [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]

Dpuiu: /* Software Packages */

2008-11-05T13:20:20Z

Software Packages

← Older revision		Revision as of 13:20, 5 November 2008
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	* [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://minisatellites.u-psud.fr/GPMS/ Microorganisms Tandem Repeats Database (Online,FR)]
	* [http://crispr.u-psud.fr/Server/CRISPRfinder.php/ CRISPRfinder (Online,FR)]		* [http://crispr.u-psud.fr/Server/CRISPRfinder.php/ CRISPRfinder (Online,FR)]; [http://nar.oxfordjournals.org/cgi/content/full/gkm360v2 Article]

Dpuiu at 11:16, 5 November 2008

2008-11-05T11:16:37Z

← Older revision		Revision as of 11:16, 5 November 2008
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	= ~~Packages~~ =		= 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)]

Dpuiu: /* Packages */

2008-11-04T21:36:45Z

Packages

← Older revision		Revision as of 21:36, 4 November 2008
Line 4:		Line 4:
	* [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