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RepeatModeler ============= Arian Smit, Robert Hubley - Institute for Systems Biology RepeatModeler is a de novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Prerequisites ------------- Perl Available at http://www.perl.org/get.html. Developed and tested with version 5.8.8. RepeatMasker & Libraries Developed and tested with open-4.0.7. The program is available at http://www.repeatmasker.org/RMDownload.html and is distributed with a minimal library set ( Dfam_consensus ). A larger set of libraries are available from http://www.girinst.org. RECON - De Novo Repeat Finder, Bao Z. and Eddy S.R. Developed and tested with our patched version of RECON ( 1.08 ). The 1.08 version fixes problems with running RECON on 64 bit machines and supplies a workaround to a division by zero bug along with some buffer overrun fixes. The program is available at: http://www.repeatmasker.org/RECON-1.08.tar.gz. The original version is available at http://eddylab.org/software/recon/. RepeatScout - De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.5 ). This version is available at http://www.repeatmasker.org/RepeatScout-1.0.5.tar.gz TRF - Tandem Repeat Finder, G. Benson et al. You can obtain a free copy at http://tandem.bu.edu/trf/trf.html. RepeatModeler was developed using 4.0.4. And one or both of the following: RMBlast - A modified version of NCBI Blast for use with RepeatMasker and RepeatModeler. Precompiled binaries and source can be found at http://www.repeatmasker.org/RMBlast.html or WUBlast/ABBlast - Sequence Search Engine, W. Gish et al. Developed and tested with 2.0 [04-May-2006]. The latest versions of ABBlast may be downloaded from: http://blast.advbiocomp.com/licensing/ Installation ------------ 1. Uncompress and expand the distribution archive: Typically: tar -zxvf RepeatModeler-open-#.#.#.tar.gz or gunzip RepeatModeler-open-#.#.#.tar.gz tar -xvf RepeatModeler-open-#.#.#.tar 2. Configure for your site: Automatic: 1. Run the "configure" script contained in the RepeatModeler distribution as: perl ./configure By Hand: 1. Copy the file "RepModelConfig.pm.tmpl" to "RepModelConfig.pm" 2. Edit the configuration parameters with a text editor. Example Run ----------- In this example we first downloaded elephant sequences from Genbank ( approx 11MB ) into a file called elephant.fa. 1. Create a Database for RepeatModeler RepeatModeler uses a ABBlast/WUBlast XDF database or a NCBI DB ( depending on the search engine used ) as input to the repeat modeling pipeline. A utility is provided to assist the user in creating a single database from several types of input structures. <RepeatModelerPath>/BuildDatabase -name elephant elephant.fa Run "BuildDatabase" without any options in order to see the full documentation on this utility. There are several options which make it easier to import multiple sequence files into one database. NOTE: It is a good idea to place your datafiles and run this program suite from a local disk rather than over NFS. 2. Run RepeatModeler RepeatModeler runs several compute intensive programs on the input sequence. For best results run this on a machine with a moderate amount of memory and several processors. Our typical setup was P4 - 4 cpus, 2.4Ghz, 3GB Memory, and Red Hat Linux. nohup <RepeatModelerPath>/RepeatModeler -database elephant >& run.out & The nohup is used on our machines when running long ( > 3-4 hour ) jobs. The output is saved to a file and the process is backgrounded. For typical runtimes ( can be > 2 days with this configuration ) see the run statistics section of this file. 3. Interpret the results This development version of RepeatModeler produces a voluminous amount of output. The raw output is directed to a working directory named RM_<PID>.<DATE> ie. "RM_5098.MonMar141305172005" and remains after each run for debugging purposes. At the completion of the run two files are generated: <database_name>-families.fa : Consensus sequences <database_name>-families.stk : Seed alignments The seed alignment file is in a Dfam compatible Stockholm format and may be uploaded to the new open Dfam_consensus database using the util/dfamConsensusTool.pl. See http://www.repeatmasker.org/RepeatModeler/dfamConsensusTool for details. The fasta format is useful for running quick custom library searches using RepeatMasker. Ie.: <RepeatMaskerPath>/RepeatMasker -lib <database_name>-families.fa mySequence.fa Other files produced in the working directory include: RM_<PID>.<DATE>/ round-1/ sampleDB-#.fa : The genomic sample used in this round sampleDB-#.fa.lfreq : The RepeatScout lmer table sampleDB-#.fa.rscons: The RepeatScout generated consensi sampleDB-#.fa.rscons.filtered : The simple repeat/low complexity filtered version of *.rscons consensi.fa : The final consensi db for this round family-#-cons.html : A visualization of the model refinement process. This can be opened in web browsers that support zooming. ( such as firefox ). This is used to track down problems with the Refiner.pl index.html : A HTML index to all the family-#-cons.html files. round-2/ sampleDB-#.fa : The genomic sample used in this round msps.out : The output of the sample all-vs-all comparison summary/ : The RECON output directory eles : The RECON family output consensi.fa : Same as above family-#-cons.html : Same as above index.html : Same as above round-3/ Same as round-2 .. round-n/ Recover from a failure If for some reason RepeatModeler fails, you may restart an analysis starting from the last round it was working on. The -recoverDir [<i>ResultDir</i>] option allows you to specify a diretory ( i.e RM_<PID>.<DATE>/ ) where a previous run of RepeatModeler was working and it will automatically determine how to continue the analysis. Please see the RELEASE-NOTES file for more details. RepeatModeler Statistics ------------------------ Benchmarks and statistics for runs of RepeatModeler on several sample genomes. RepeatModeler 1.0.3 ( RECON + RepeatScout ): Genome DB Sample*** Run Time* Models Models % Sample Genome Size (bp) Size (bp) (hh:mm) Built Classified Masked** ---------- ----------- ---------- ---------- ------- ----------- -------- Marmoset 3.0 Bbp 228 Mbp 55:37 582 564 36.4 Zebrafinch 1.2 Bbp 222 Mbp 66:29 178 75 8.6 * Analysis run on a 4 processor P4, 2.4Ghz, 3GB RAM, machine running Red Hat Linux. ** Includes simple repeats and low complexity DNA. Results obtained with RepeatMasker open-3.2.5, WUBlast and the -lib option. *** Sample size does not include 40 Mbp used in the RepeatScout analysis. This 40 Mbp is randomly chosen and may overlap 0-100% of the sample used in the RECON analysis. RepeatModeler 1.0.2 ( RECON + RepeatScout ): Genome DB Sample*** Run Time* Models Models % Sample Genome Size (bp) Size (bp) (hh:mm) Built Classified Masked** ---------- ----------- ---------- ---------- ------- ----------- -------- Human HG18 3.1 Bbp 238 Mbp 46:36 614 611 35.66 Platypus 1.9 Bbp 220 Mbp 76:02 540 457 Zebrafinch 1.3 Bbp 220 Mbp 63:57 233 104 9.41 Sea Urchin 867 Mbp 220 Mbp 40:03 1830 360 33.85 diatom 32,930,227 32,930,227 4:41 128 35 2.86 Rabbit 11,770,949 11,770,949 3:14 83 72 31.30 * Analysis run on a 4 processor P4, 2.4Ghz, 3GB RAM, machine running Red Hat Linux. ** Includes simple repeats and low complexity DNA. Results obtained with RepeatMasker open-3.1.9, WUBlast and the -lib option. *** Sample size does not include 40 Mbp used in the RepeatScout analysis. This 40 Mbp is randomly chosen and may overlap 0-100% of the sample used in the RECON analysis. RepeatModeler 1.0.0 ( RECON ): Genome DB Sample Run Time* Models Models % Sample Genome Size (bp) Size (bp) (hh:mm) Built Classified Masked** ---------- ----------- ---------- ---------- ------- ----------- -------- Opossum 3.5 Billion 319 Mbp 140:52 1137 467 52.55 Armadillo 47,332,136 47,332,136 6:20 121 92 36.07 Platypus 14,768,992 14,768,992 3:46 18 13 40.69 Rabbit 11,770,949 11,770,949 2:17 20 16 28.67 Elephant 11,550,090 11,550,090 1:21 34 28 37.08 * Analysis run on a 4 processor P4, 2.4Ghz, 3GB RAM, machine running Red Hat Linux. ** Includes simple repeats and low complexity DNA. Results obtained with RepeatMasker open-3.0.9, WUBlast and the -lib option. Caveats ------- o Genomes with numerous short contigs ( Diatom for example ) will take longer to BLAST than larger genomes with larger contigs. This is an optimization problem left for future releases. o This program is not parallelized. It can only run on one node. This is something we are considering for future releases. Credits ------- Arnie Kas for the work done on the original MultAln.pm. Andy Siegel for statistics consultations. Thanks so much to Warren Gish for his invaluable assistance and consultation on his WUBlast program suite. Alkes Price and Pavel Pevzner for assistance with RepeatScout and hosting my multi-sequence version of RepeatScout. This work was supported by the NIH ( R44 HG02244-02), and the Institute for Systems Biology. License ------- This work is licensed under the Open Source License v2.1. To view a copy of this license, visit http://www.opensource.org/licenses/osl-2.1.php or see the LICENSE file contained in this distribution.