Magic-Enzyme-Cutter:Magic-Enzyme-Cutter is a software that Master Restriction Enzyme II digestion in silico && Evaluate the degradation products in many aspects && Calculate the optimal selection in expect (MEC)
Perl 98.31%Shell 1.69%
mec's Introduction
-------------------------
Magic-Enzyme-Cutter (MEC)
-------------------------
Author :
Mao Fengbiao
Contact:
[email protected].
Version:
1.0.
License:
GPLv3 (http://www.gnu.org/licenses/gpl.html)
--------------------
Software description
--------------------
Magic-Enzyme-Cutter is a software that Master Restriction Enzyme II
digestion in silico && Evaluate the degradation products in many aspects &&
Calculate the optimal selection in expect (MEC).
------------------------
Platform and environment
------------------------
System: Linux or UNIX
Software: perl >= v5.8.8, R >= R-2.15.1 are required.
perl download website : http://www.perl.org/
R download website : http://www.r-project.org/
--------------
How to run MEC
--------------
1. Install the software
>tar xzvf MEC-xxx.tar.gz
>cd MEC-xxx
>sh install /path/to/R
2. Run the software
>cd MEC-xxx
>./Magic-Enzyme-Cutter -help
3. Test the software
>cd MEC-xxx/test
>sh test.sh /path/to/R
Results of test are in directory 'MEC-xxx/test/test-result'
More information is available in file 'MEC-xxx/Manual' and
in directory 'MEC-xxx/doc' which contains *doc files or PDF
files about introduction and manual.
-------------------
Magic-Enzyme-Cutter
-------------------
Master Restriction Enzyme II digestion in silico && Evaluate the
degradation products in many aspects && Calculate the optimal selection in
expect (MEC).
Author : Mao FengBiao,Cai WanShi,Wen YanLing.
Contact: [email protected].
Version: 1.0.
Usage:
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> [options]
Require:
-i <in_file: reference in FASTA format>
-o <out_directory>
Options:
-R <R path> [R]
-z <enzyme name or cut-Type> [MspI]
-m <motif which is focus on> [CG]
-s <start length of fragment> [40]
-e <end length of fragment> [1000]
-n <min regions of PSO search> [200]
-x <max regions of PSO search> [500]
-f <bases of flanking included> [4]
-g <graduated scale number> [100]
-c <change the vision,T or F> [F]
-t <transparency of Gel Figure> [50]
-h <display this help information>
Note:
The delimiter of enzymes is ",", "_" or "+" while the delimiter of
cut-Type is "-".
The brief-codes of cut-Type are supported, They are:
R=G/A;Y=C/T;M=A/C;K=G/T;S=G/C;W=A/T;B=C/G/T;D=A/G/T;H=A/C/T;V=A/C/G;N=A/C/G/T.
Gzipped FASTA format input is supported.
Example:
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> -z MspI -s 100 -e 2000
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> -R /Path/R -z C-CGG,C-GGC,G-CGC
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> -R /Path/R -z MspI_AciI+TaqI
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> -R /Path/R -z MspI+TTT-AAA+YAC-GTR
Magic-Enzyme-Cutter -i <ref.fa> -o <outdir> -n 100 -x 300 -g 50 -f 5 -c T
The FASTA format file of sequences. See example data:
>chrR
GATCTGATAAGTCCCAGGACTTCAGAAGagctgtgagaccttggccaagt
cacttcctccttcagGAACATTGCAGTGGGCCTAAGTGCCTCCTCTCGGG
ACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT
TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAA
AGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCA
AATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTG
GATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGAT
TTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACCAATTTGGAAA
TATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATctt
cccatttatataaatacttgcaagtagtagtgccataattaccaaacata
aagccaactgagatgcccaaagggggccactctccttgcttttcctcctt