NAME - Run the LTRFinder program in batch mode


This documentation refers to program version $Rev: 558 $


Usage -i InDir -o OutDir -c ConfigFile

Required Arguments

    -i,--indir    # Directory of fasta files to process
    -o,--outdir   # Path to the base output directory
    -c,--config   # Path to the config file


This program will run the LTR_FINDER program for a set of fasta files. You can set multiple parameter sets using a config file.



Path of the directory containing the sequences to process.


Path of the directory to place the program output.


Path to the batch_ltrfinder config file. This is a tab delimited text file made up of two columns. The first column indicates the name assigned to the parameter set, while the second column contains the flags that will be passed to the LTR_FINDER program.



Path to the LTR_FINDER binary.


Path to the tRNA database used by LTR_FINDER. This file is part of the LTR_FINDER download.


Path to the prosite directory for use by LTR_FINDER.


Convert the outout to gff format.


Extract sequence string of features. These will be extracted as separate fasta files for each sequence feature class. These fasta files will be stored in the ltr_finder directory. Using rootname as the name of the contig and ltrid as the number assigned by LTR_Finder, the fasta files that are created are:


The sequence of the five prime LTR. This is not extracted from the alignment returned by LTR_Finder, but is extracted from the original sequence using the coordinates returned by LTR finder.


The squence of the three primer LTR. This is also extracted from the original sequence using the coordinates returned by LTR finder.


The name of the individual LTR retrotransposon identified will be consistant across these fasta files. Not all


Short overview of how to use program from command line.


Show program usage with summary of options.


Show program version.


Show the full program manual. This uses the perldoc command to print the POD documentation for the program.


Run the program in verbose mode.


Run the program with minimal output.


The list of error messages that can be generated, explanation of the problem one or more causes suggested remedies list exit status associated with each error


Configuration File

The location of the configuration file is indicated by the --config option at the command line. This is a tab delimited text file allowing you to run the LTR_FINDER program with multiple parameter sets for each query sequence file. This config file is a two column file. Lines beginning with the # symbol are ignored and provide a way to add comments to your config file. This config file is expected to have UNIX format line endings. You should therefore avoid creating config files using Windows based programs such as MS Word.

Col 1. Parameter set name

This is the name assigned to the parameter set defined on the current line. This name must not have any spaces. This name will be appended to the output gff file.

Col 2. LTR_FINDER Options

A string of command line options to send to the LTR finder program. For a full set of possible variables, see the LTR_FINDER User Manual

Example config file:

   # Simple batch_ltrfinder config file
   p_30 -p 30
   p_10 -p 10
   # END

User Environment

This program makes use of the following variables defined in the user's environment.


This is the path to TRNA_DB used by LTR_FINDER.


This is the path to the directory of Prosite models use by LTR_FINDER.


This is the path to the LTR_FINDER binary.

Example environment variables set in the bash shell:

   export TRNA_DB='/home/yourname/apps/LTR_Finder/tRNAdb/Os-tRNAs.fa'
   export PROSITE_DIR='/home/yourname/Apps/LTR_Finder/ps_scan'
   export LTR_FINDER='ltr_finder'


Required Software

Required Perl Modules


The program is part of the DAWG-PAWS package of genome annotation programs. See the DAWG-PAWS web page ( ) or the Sourceforge project page ( ) for additional information about this package.





A manuscript is being submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program:

JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes.




James C. Estill <JamesEstill at>


STARTED: 10/02/2007

UPDATED: 03/24/2009

VERSION: $Rev: 558 $