getx.py generates mutation fragments and provides files useful to perform the
facile genome modification method described in "A versatile and highly
efficient method for scarless genome editing in Escherichia coli and Salmonella
enterica (2014), BMC Biotechnology 14:84, DOI: 10.1186/1472-6750-14-84."
CITATION
Please cite the original manuscript below for genome editing methods and procedure.
"A versatile and highly
efficient method for scarless genome editing in Escherichia coli and Salmonella
enterica (2014), BMC Biotechnology 14:84, DOI: 10.1186/1472-6750-14-84."
Please refer to the following link to cite for the python script.
"https://sourceforge.net/projects/getx/"
INSTALLATION AND RUNNING THE SCRIPT
getx is written and tested with python 2.7.6 and biopython 1.63 on OSX 10.6.8.
Standalone executable versions were tested on Mac OS X 10.6 (64 bit),
Ubuntu 12.04.4 (64 bit), and on Windows 7 (32 bit).
Current version may not work with other version of python or biopython.
Copy the getx.py script and the following genbank files (pHA1887_4.gb, T2ISceI_C_2.gb,
T2ISceI_K_2.gb, T2ISceI_T_2.gb, and T2ISceI_C2_2.gb) in a folder. Download a genbank or
a fasta file of the target genome that the user wish to modify. Run the script by executing
the script by python, “python getx.py”.
USE OF OUTPUT FILES
getX will generate seven files into the same folder where the user runs the script including
three individual fasta files for a mutation cassette template plasmid, for a mutation cassette,
and a small region of genome surrounding the mutation, three individual genbank files for
the same above, and a “.tab” file including the 5’-mutation fragment and 3’-mutation fragment
sequences, sequences of PCR primers required to amplify a mutation cassette from its template
plasmid. We recommend the user to examine three genbank files to confirm the design using
a genbank file viewer. We have been using CLC Main workbench (available from Qiagen Bioinformatics)
successfully to examine the genbank files and later to confirm the sequence of plasmids and to
confirm sequence surrounding the part of the genome manipulated. We also recommend to design
a set of PCR primers surrounding the region manipulated manually to confirm the mutants created.
The script is not designed to generate the latter primers.
LICENSE
Copyright 2017 by The Regents of the University of Colorado.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software
and associated documentation files (the "Software"), to deal in the Software without restriction,
including without limitation the rights to use, copy, modify, merge, publish, distribute,
sublicense, and/or sell copies of the Software, and to permit persons to whom the Software
is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or
substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
