Wikiomics:Repeat finding - Revision history

Darek Kedra: /* References */

Darek Kedra — Thu, 02 Dec 2010 12:06:04 GMT

References

←Older revision		Revision as of 12:06, 2 December 2010
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	==Others==		==Others==
	* seg from wu-blast		* seg from wu-blast
		+
		+	=ribosomal RNA detection=
		+	While not "repetitive" in a strict sense, ribosomal sequences need to be detected and preferably masked for i.e. de novo gene prediction or ESTs mapping. There are in Genbank "protein coding genes" predicted from ribosomal sequences, not only as a result of de novo prediction but "prediction with a strong ESTs/RNA-Seq support".
		+
		+	==RNAmmer==
		+	http://www.cbs.dtu.dk/services/RNAmmer/
		+
		+	Wildly used.
		+
		+	==Meta-RNA==
		+	http://tools.camera.calit2.net/camera/meta_rna/
		+
		+

	=References=		=References=

Darek Kedra: /* References */

Darek Kedra — Thu, 30 Sep 2010 10:07:12 GMT

References

←Older revision		Revision as of 10:07, 30 September 2010
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	For pages on similar topics visit: [http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]		For pages on similar topics visit: [http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]
		+
		+	=De novo masking without library=
		+
		+	These programs can mask sequence using only sequence itself.
		+
		+	==Tandem Repeats Finder==
		+	web: http://tandem.bu.edu/trf/trf.html
		+	current version: 4.04
		+
		+	Options recommended for genome 2 genome alignments in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829014/
		+
		+	match = 2 mismatch = 5 delta = 5 PM = 80 PI = 10 minscore = 30 maxperiod = 200 -R
		+
		+	==DustMasker==
		+	http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker/
		+
		+	==WindowMasker==
		+	http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/
		+
		+	==Others==
		+	* seg from wu-blast

	=References=		=References=

Darek Kedra: /* RepeatMasker */

Darek Kedra — Fri, 20 Aug 2010 12:53:31 GMT

RepeatMasker

←Older revision		Revision as of 12:53, 20 August 2010
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	-el(egans) masks repeats found in C. elegans		-el(egans) masks repeats found in C. elegans
	</pre>		</pre>
		+
		+
		+	==TransposonPSI==
		+
		+	* web site: http://transposonpsi.sourceforge.net/
		+	* latest version: 08-19-2010
		+	"identifies protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements using PSI-blast"
		+
		+	Rather slow in sequential mode for larger genomes. Speedups easily obtainable by splitting the target genome/proteome and running it on multiple nodes and/or modifying transposonPSI.pl script by adding "-a number_of_cores" (number_of_cores -> number, i.e. 4) to two lines executing blast searches. GFF3 output.

	=De novo repeat library construction=		=De novo repeat library construction=

Darek Kedra: /* ReAS (broken install) */

Darek Kedra — Fri, 30 Jul 2010 21:19:29 GMT

ReAS (broken install)

←Older revision		Revision as of 21:19, 30 July 2010
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	tar xfvz ReAS_2.02.tar.gz; cd ReAS_2.02/code		tar xfvz ReAS_2.02.tar.gz; cd ReAS_2.02/code
	</pre>		</pre>
-	* open N_matchreads.cpp and add line below i.e. after "#include<time.h>":	+
		+	* fix two files:
		+	open code/N_matchreads.cpp and add line below i.e. after "#include<time.h>":
	<pre>		<pre>
	#include <cmath>		#include <cmath>
	</pre>		</pre>
		+
		+	perltidy finds one error in Clustering.pl. Replace:
		+	<pre>
		+	my $cluster_dir "cluster_"; #prefix of directory names
		+	</pre>
		+
		+	with:
		+
		+	<pre>
		+	my $cluster_dir = "cluster_"; #prefix of directory names
		+	</pre>
		+
		+
	* compile ReAS		* compile ReAS
	<pre>		<pre>
Line 191:		Line 206:
	</pre>		</pre>

-	~~Also perltidy finds one error in Clustering.pl. Replace:~~	+	* you need to have on your PATH
-	~~<pre>~~	+	** dust from wublast, unknown version (not tested yet with dustmasker from blast)
-	~~my $cluster_dir "cluster_"; #prefix of directory names~~	+	** muscle (3.6 was used originally)
-	~~</pre>~~	+	** cross_match.manyreads from phrap

-	with:	+	With a large number of reads and "-pa 1" (see below) cross_match (version: 0.990329) crashes with: "FATAL ERROR: seq_area_size".
		+	Untested:
		+	* the newest beta version (1.090518) do not have this memory limit, but also do not have cross_match.manyreads(?)
		+	* in the older version of cross_match one can change #define BLOCK_SIZE 10000 in db.c and recompile

		+	* I decreased the input size for testing (265Mb fasta with 592k 454 reads) which is small enough. Possibly running ReAS with
	<pre>		<pre>
-	~~my $cluster_dir = "cluster_"; #prefix of directory names~~	+	reas_all.pl -read input.fasta -n 8
	</pre>		</pre>
		+
		+	may fix it.

	====Usage====		====Usage====
-
-	* you need to have on your PATH
-	** dust from wublast (not tested yet with dustmasker from blast)
-	** muscle
-	** cross_match from phrap

	read 00readme located in ReAS_2.02/code for more detailed instructions.		read 00readme located in ReAS_2.02/code for more detailed instructions.

-	To run ~~on 8 CPU cores~~ with ~~otherwise~~ default settings with already selected set of reads:	+	To run with default settings with already selected set of reads:
	<pre>		<pre>
-	nohup reas_all.pl -read 454_subset_4repeat_search.fas ~~-pa 8~~ -output 454_subset_4repeat_search.fas.cons_reas 2 > nohup.reas1.txt &	+	nohup reas_all.pl -read 454_subset_4repeat_search.fas -output 454_subset_4repeat_search.fas.cons_reas 2 > nohup.reas1.txt &
	</pre>		</pre>

-	CAVEAT: at the current stage above command does not run all scripts ~~(on my computer: multi_run2.sh: line 72: dust: command not found)~~.	+	CAVEAT: at the current stage above command does not run all scripts correctly.
		+

	====external info====		====external info====

Darek Kedra: /* Installation */

Darek Kedra — Fri, 30 Jul 2010 18:58:12 GMT

Installation

←Older revision		Revision as of 18:58, 30 July 2010
Line 191:		Line 191:
	</pre>		</pre>

-	Also perltidy finds one error in Clustering.pl:	+	Also perltidy finds one error in Clustering.pl. Replace:
-	Replace:	+
	<pre>		<pre>
	my $cluster_dir "cluster_"; #prefix of directory names		my $cluster_dir "cluster_"; #prefix of directory names
	</pre>		</pre>
		+
		+	with:

	<pre>		<pre>

Darek Kedra: /* Installation */

Darek Kedra — Fri, 30 Jul 2010 18:57:30 GMT

Installation

←Older revision		Revision as of 18:57, 30 July 2010
Line 189:		Line 189:
	<pre>		<pre>
	export PATH=/your/path/to/ReAS_2.02/bin/:$PATH		export PATH=/your/path/to/ReAS_2.02/bin/:$PATH
		+	</pre>
		+
		+	Also perltidy finds one error in Clustering.pl:
		+	Replace:
		+	<pre>
		+	my $cluster_dir "cluster_"; #prefix of directory names
		+	</pre>
		+
		+	<pre>
		+	my $cluster_dir = "cluster_"; #prefix of directory names
	</pre>		</pre>

Darek Kedra: /* Usage */

Darek Kedra — Tue, 13 Jul 2010 12:45:10 GMT

Usage

←Older revision		Revision as of 12:45, 13 July 2010
Line 207:		Line 207:
	CAVEAT: at the current stage above command does not run all scripts (on my computer: multi_run2.sh: line 72: dust: command not found).		CAVEAT: at the current stage above command does not run all scripts (on my computer: multi_run2.sh: line 72: dust: command not found).

-	~~For pages on similar topics visit~~: ~~[http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]~~	+	====external info====
		+	* There is description how ReAS was used in Hydra magnipapillata genome project (see supplementary information PDF, section "S9. Analysis of repeated sequences"):

-	<!-- ~~other contributors~~, ~~put yourself here~~ -->	+	http://www.nature.com/nature/journal/v464/n7288/full/nature08830.html
		+
		+	From 10M+ Sanger sequences of average length 800+ bp they constructed two libraries:
		+	* A) 1% of reads, 17-mers with a depth of at least 10 ("especially enriched in the CR1 class of retrotransposons")
		+	* B) 10% of reads 17-mers depth range of 10 to 100.
		+
		+	"""
		+	- to improve the quality of the assembly, only reads that have at least 100 high-depth 17-mers were considered
		+
		+	- ReAS was run on each of the libraries separately
		+
		+	- after retaining only the assembled repeats of length larger than 500 nucleotides and a minimal average depth value (as provided by the
		+	program) of 10, the two libraries contained 949 and 25,110 repeats each, respectively.
		+
		+	- These sequences were then pulled together.
		+
		+	- initial ReAS assembly appears to be fragmented and there are many redundant sequences, the final version of the library was produced by
		+	running ReAS' join_fragments.pl and rmRedundance.pl scripts.
		+
		+	- final library contained 3909 reconstructed repetitive elements with an average length of about 1500 nt.
		+	"""
		+
		+	* see this thread @Biostar:
		+	http://biostar.stackexchange.com/questions/753/instaling-reas-repeat-finding
		+
		+
		+
		+	For pages on similar topics visit: [http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]

	=References=		=References=

Darek Kedra: /* ReAS */

Darek Kedra — Wed, 12 May 2010 08:11:43 GMT

ReAS

←Older revision		Revision as of 08:11, 12 May 2010
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	This is pre-assembly repeat finding method.		This is pre-assembly repeat finding method.

-	===ReAS===	+	===ReAS (broken install)===
	[http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010043 Paper]		[http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010043 Paper]
	====Installation====		====Installation====

Darek Kedra: +Bergman

Darek Kedra — Tue, 20 Apr 2010 13:52:29 GMT

+Bergman

←Older revision		Revision as of 13:52, 20 April 2010
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	Task A is usually a prerequisite step for genome annotation and even blast searches. For newly sequences genomes one should start with B (constructing species specific repeat library).		Task A is usually a prerequisite step for genome annotation and even blast searches. For newly sequences genomes one should start with B (constructing species specific repeat library).

		+	For more comprehensive list of programs read [http://bergmanlab.smith.man.ac.uk/?page_id=295 TE tools@Bergman Lab, U. of Manchester, UK]

	=Detecting known repeats=		=Detecting known repeats=
Line 51:		Line 52:
	For programs recommendations based on test see: Saha et al. [http://nar.oxfordjournals.org/cgi/content/full/gkn064v1 Empirical comparison of ab initio repeat finding programs] (2008)		For programs recommendations based on test see: Saha et al. [http://nar.oxfordjournals.org/cgi/content/full/gkn064v1 Empirical comparison of ab initio repeat finding programs] (2008)

-	For an extensive ~~review~~ listing tens of programs: Lerat E.[http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy2009165a.html Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs ] (Nov 2009)	+	For an extensive reviews listing tens of programs:
		+	* Bergamn C. [http://bib.oxfordjournals.org/cgi/content/full/8/6/382 Discovering and detecting transposable elements in genome sequences] (2007)
		+	* Lerat E. [http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy2009165a.html Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs ] (Nov 2009)

	Keep in mind that resulting libraries should be further screened for gene families. There are border cases, where genome may contain thousands of modified copies of a gene, ranging from seemingly functional copies, through pseudogenes, gene fragments and single exons (i.e Speer family in rodents).		Keep in mind that resulting libraries should be further screened for gene families. There are border cases, where genome may contain thousands of modified copies of a gene, ranging from seemingly functional copies, through pseudogenes, gene fragments and single exons (i.e Speer family in rodents).

Darek Kedra: /* Usage */

Darek Kedra — Fri, 16 Apr 2010 11:08:48 GMT

Usage

←Older revision		Revision as of 11:08, 16 April 2010
Line 202:		Line 202:
	</pre>		</pre>

		+	CAVEAT: at the current stage above command does not run all scripts (on my computer: multi_run2.sh: line 72: dust: command not found).

	For pages on similar topics visit: [http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]		For pages on similar topics visit: [http://openwetware.org/wiki/Wikiomics Wikiomics@OpenWetWare]