This directory contains the source code for the TAL Effector Site Finder.
All source code is available under an ISC license.
Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
TALESF is a C library for identifying potential binding sites for transcription activator-like (TAL) effectors in a given genomic sequence. Compiling and running this program requires a C compiler with OpenMP support (such as GCC 4.2 or higher). libbcutils must also be installed. To compile TALESF, enter the following commands in the directory containing this file:
make make install make frontend
cd cython_wrapper python setup.py build_ext python setup.py install
After compiling, you can run the program like this:
./talesf -o output_file genome_seq.fasta "NN HD NI HG HD NG N* HD HD NI NG NG NI HD NG NN NG NI NI NI NI N* NS N*"
This command will search the genome sequence saved in the file genome_seq.fasta for RVD sequence "NN HD NI HG HD NG N* HD HD NI NG NG NI HD NG NN NG NI NI NI NI N* NS N*" and save the output in files called output_file.txt and output_file.gff3. Note that the file genome_seq.fasta must be in FASTA format.
For information on available options:
By default, the output data is sorted by score. The 'sortfilter' script is provided as a tool for (surprise!) sorting and filtering output from TALESF. For a descriptive usage statement, enter the following command.