It's about synthetic biology - specifically, designing constructs up to 10kb in
To install this module, run the following commands:
Answer the following questions (may differ based on your system, [defaults]):
Where should GeneDesign write tmp files? [ /tmp ]
Where should GeneDesign config files be installed? [ /etc/GeneDesign/ ]
Should GeneDesign install scripts? [ Y ]
Where should GeneDesign scripts be installed? [ /usr/local/bin/ ]
Enable GD::Graphics support? [ Y ]
Enable EMBOSS palindrome for hairpin detection? [ Y ]
Enable BLAST+ for similarity detection (SLOW)? [ Y ]
Enable vmatch for similarity detection (LESS SLOW)? [ Y ]
You may need to install some additional perl modules for it to work:
Then run the following:
Then enjoy GeneDesign.
OH NO, VMATCH
Are you trying to use Vmatch with GeneDesign? Are you getting these kinds of
--------------------- WARNING ---------------------
MSG: Use of method no_sequences() is deprecated, use num_sequences() instead
To be removed in 1.0075
UNIVERSAL->import is deprecated and will be removed in a future perl at
Bio/Grep/Backend/BackendI.pm line 37.
These are caused by code in the parsing package GeneDesign uses to read Vmatch
output. To remove these (harmless but annoyingly persistent) warnings, use the
patches in the BioGrepPatch folder. Bio::Grep::BackendI needs to be patched as
described in BackendI.patch, and Bio::Grep::Backend::Vmatch needs to be patched
as described in Vmatch.patch.
SUPPORT AND DOCUMENTATION
After installing, you can find documentation for this module with the
You can also look for information at:
RT, CPAN's request tracker (report bugs here)
AnnoCPAN, Annotated CPAN documentation
COPYRIGHT AND LICENSE
Copyright (c) 2013, GeneDesign developers
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.
* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley
National Laboratory, the Department of Energy, and the GeneDesign developers may
not be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.