#GuideMaker
Globally design gRNAs for any CRISPR-Cas system in any small genome
Authors
- Lidimarie Trujillo, Department of Microbiology and Cell Science, University of Florida
- Ravin Poudel, PhD, Department of Microbiology and Cell Science, University of Florida
- Christopher Reisch, PhD, Department of Microbiology and Cell Science, University of Florida
- Adam R. Rivers, PhD , US Department of Agriculture, Agricultural Research Service
Introduction
Installation
GuideMaker can be installed from:
- The Github repository: https://github.com/USDA-ARS-GBRU/guidemaker
git clone https://github.com/USDA-ARS-GBRU/guiemaker.git
Dependencies
Following are the required softwares/programs.
pybedtools
NMSLib
Biopython
Pandas
Usage
GuideMaker: globally design guide RNAs for any CRISPR-Cas system in any genome
optional arguments:
-h, --help show this help message and exit
--genbank GENBANK [GENBANK ...], -i GENBANK [GENBANK ...]
One or more genbank .gbk or gzipped .gbk files for a
single genome
--pamseq PAMSEQ, -p PAMSEQ
A short PAM motif to search for, it may use IUPAC
ambiguous alphabet
--outfile OUTFILE, -o OUTFILE
The table of PAM sites and data
--pam_orientation {5prime,3prime}, -r {5prime,3prime}
PAM position relative to target: 5prime:
[PAM][target], 3prime: [target][PAM]. For example,
Cas9 is 3prime
--guidelength [10-27], -l [10-27]
Length of the guide sequence
--strand {forward,reverse,both}, -s {forward,reverse,both}
Strand of DNA to search
--lcp [0-27] Length of the guide closest to the PAM required to be
unique
--dist [1-5] Minimum hamming distance from any other potential
guide
--before [1-500] keep guides this far in front of a feature
--into [1-500] keep guides this far inside (past the start site)of a
feature
--knum [2-20] how many sequences similar to the guide to report
--threads THREADS The number of cpu threads to use
--log LOG Log file
--tempdir TEMPDIR The temp file directory
-V, --version show program's version number and exit
Examples
Use case: Retrieving target sequence for a given PAM motif in the forward and reverse strands, where length of guide sequence is 20 base pair. 12 base pair close to PAM motif is conserved ,i.e. unique and the full sequence has a hamming distance of more than 2. Here the number of used threads is 2 Return a table of pam sites and associated data, at in current folder.
guidemaker -i sample.gbk -p NGG --targetlength 20 --strand both \
--lcp 10 --dist 2 --outfile out.txt \
--log logfile.txt --threads 2
API documentation
API documentation for the module can be found here
License information
As a work of the United State Governemnt this software is available under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication