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findltr

Command-line tool for de novo identification of LTR retrotransposons.

Requirements

  • Basic Local Alignment Search Tool (BLAST):

    $ sudo apt-get install ncbi-blast+

  • Genome Tools(GT) with enabled HMMER option(with-hmmer=yes) via compilation.

Installations

Example install, using VirtualEnv:

# install/use python virtual environment
virtualenv ~/virtenv_scratch --no-site-packages

# activate the virtual environment
source ~/virtenv_scratch/bin/activate

# upgrade pip in the new virtenv
pip install -U pip setuptools

# install this package in DEVELOPMENT mode
python setup.py develop

# or simply install
# python setup.py install

Options

The list of available options:

General
--input Input *.fasta or *.fa file
--output Output *.gff file
Search parameters
Option Description Default
--algorithm Algorithm, [kmp|salcp|original] original
--pattern_len Length of pattern 20
--min_distance Minimal distance between LTRs 1000
--max_distance Maximal distance between LTRs 20000
--min_ltr_len Minimal length of LTRs 100
--max_ltr_len Maximal length of LTRs 1000
Other
--verbose Include more details
--debug Turn on debugging output, do not catch exceptions

See findltr --help for complete list of available options.