RepeatModeler Download Page

RepeatModeler - Beta 1.0.3

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-3.2.2. This version must be used with open-3.2.2 or greater of RepeatMasker. The program is available at http://www.repeatmasker.org/RMDownload.html and the libraries are at http://www.girinst.org.
RECON - De Novo Repeat Finder, Bao Z. and Eddy S.R.
Developed and tested with our patched version of RECON ( 1.06 ). The 1.06 version fixes problems with running RECON on 64 bit machines. The program is available at: http:://www.repeatmasker.org/RECON1.06.tar.gz. The original version is available at http://selab.janelia.org/recon.html.
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 ( 1.0.4 ). This version is now available at http://repeatscout.bioprojects.org/.
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 3.2.1.
WUBlast - Sequence Search Engine, W. Gish et al.
Developed and tested with 2.0 [04-May-2006]. The program can be downloaded at http://blast.wustl.edu/.

RepeatModeler Installation

Download RepeatModeler
Latest Version Released 5/1/2008: RepeatModeler-open-1-0-3.tar.gz
Unpack Distribution
Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /usr/local/ ).
- cp RepeatModeler-open-1-#-#.tar.gz /usr/local
- cd /usr/local
- gunzip RepeatModeler-open-1-#-#.tar.gz
- tar xvf RepeatModeler-open-1-#-#.tar
Configure for your site
Automatic:
- Run the "configure" script contained in the RepeatModeler distribution as: perl ./configure
By Hand:
- Copy the file "RepModelConfig.pm.tmpl" to "RepModelConfig.pm"
- 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.

Create a XDF Database for RepeatModeler RepeatModeler uses the WUBlast XDF database as input to the repeat modeling pipeline. A utility is provided to assist the user in creating a single XDF database from several types of input structures.
[RepeatModelerPath]/BuildXDFDatabase -name elephant elephant.fa
Run "BuildXDFDatabase" 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.
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.

Interpret the results This development version of RepeatModeler produces a voluminous amount of output. The output is directed to a working directory named RM_[PID].[DATE] ie. "RM_5098.MonMar141305172005". In the working directory the final product, a file named "consensi.fa.classified" can be found. This is formatted as a RepeatMasker library and may be used directly with RepeatMasker as:

[RepeatMaskerPath]/RepeatMasker -lib consensi.fa.classified mySequence.fa

Other files produced in the working directory include:

       RM_./
          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/

Benchmarks

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
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.

Caveats

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.
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 HG02244-05), and the Institute for Systems Biology.

License

RepeatModeler "open-1.0" is licensed under the Open Source License v2.1.