You can also download portable version of Cas-OFFinder!

To download and run Cas-OFFinder, please follow below instructions.

STEP 1

Cas-OFFinder requires an OpenCL-enabled device (CPU, GPU, or etc..) and corresponding runtime driver pre-installed to run properly.

Please download and install the latest driver below:

Before installing Cas-OFFinder, please check whether your device is an OpenCL-supported one.

Khronos group provides an extensive list of OpenCL supported devices here.

Supported OS

STEP 2

Whole genome of target organism is needed (in FASTA format). You can find one in one of the below links:

Extract all FASTA files in a directory. Remember the full path of the FASTA files directory.

STEP 3

Download Cas-OFFinder Binary here.

(Its source code is accessible on Github, or downloadable as zip file. But if you want to just use Cas-OFFinder, you don't need to download source code files)

NOTE: It is reported that Cas-OFFinder sometimes hangs with certain version of AMD driver due to unknown reason. If you experience this issue, then please try older version of Cas-OFFinder, or use Cas-OFFinder on the system with GPUs/accelerators of other vendors. We are currently examining this issue, and we will release revised version of Cas-OFFinder as soon as we fix it.

STEP 4 - Usage

Basic usage of Cas-OFFinder is following:

cas-offinder {input_file_path} {G or C} {output_file_path}

G stands for using all available GPU devices, and C for using all CPUs.

Input file

Note that Cas-OFFinder allows mixed bases to account for the degeneracy in PAM sequences and the number of mismatched bases is not limited!

Following codes are supported for the bases:

CodeBase
AAdenine
CCytosine
GGuanine
TThymine
CodeBase
RA or G
YC or T
SG or C
WA or T
KG or T
MA or C
CodeBase
BC or G or T
DA or G or T
HA or C or T
VA or C or G
Nany base

An example of input file:

/var/chromosomes/human_hg19
NNNNNNNNNNNNNNNNNNNNNRG
GGCCGACCTGTCGCTGACGCNNN 5
CGCCAGCGTCAGCGACAGGTNNN 5
ACGGCGCCAGCGTCAGCGACNNN 5
GTCGCTGACGCTGGCGCCGTNNN 5
...

Now you can run Cas-OFFinder as following:

cas-offinder input.txt G out.txt

If you get an error message "command not found", try adding a ./ before the cas-offinder.

Output file

An example of output file:

GGCCGACCTGTCGCTGACGCNNN chr8 49679    GGgCatCCTGTCGCaGACaCAGG + 5
GGCCGACCTGTCGCTGACGCNNN chr8 517739   GcCCtgCaTGTgGCTGACGCAGG + 5
GGCCGACCTGTCGCTGACGCNNN chr8 599935   tGCCGtCtTcTCcCTGACGCCAG - 5
GGCCGACCTGTCGCTGACGCNNN chr8 5308348  GGCaGgCCTGgCttTGACGCAGG - 5
GGCCGACCTGTCGCTGACGCNNN chr8 9525579  GGCCcAgCTGTtGCTGAtGaAAG + 5
GGCCGACCTGTCGCTGACGCNNN chr8 12657177 GGCCcACCTGTgGCTGcCcaTAG - 5
GGCCGACCTGTCGCTGACGCNNN chr8 12808911 GGCCGACCaGgtGCTccCGCCGG + 5
GGCCGACCTGTCGCTGACGCNNN chr8 21351922 GGCCcACCTGaCtCTGAgGaCAG - 5
GGCCGACCTGTCGCTGACGCNNN chr8 21965064 GGCCGtCCTGcgGCTGctGCAGG - 5
GGCCGACCTGTCGCTGACGCNNN chr8 22409058 GcCCGACCccTCcCcGACGCCAG + 5
...