1. Daniel Standage
  2. TALESF

Overview

This directory contains the source code for the TAL Effector Site Finder.

With the exception of the Kseq library (self-contained in the `kseq.h' file),
all source code included herein is available under an ISC license.

Copyright (c) 2011-2012, Daniel S. Standage <daniel.standage@gmail.com> and
Erin Doyle <edoyle@iastate.edu>.

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 program 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). To compile TALESF, enter the following command in the directory
containing this file.

  gcc -Wall -O3 -m64 -o talesf *.c -lm -lz -fopenmp

For a descriptive usage statement, enter the following command.

  ./talesf -h

By default, the output data is sorted by genomic position. If multiple
processors are used, binding sites from different sequences will be
interspersed in the output. 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.

  ./sortfilter -h