MysiRNA source code for Academic Users, Version 1
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License Terms
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The MysiRNA Designer Code and scripts for Academic Users is a software for design of siRNA.
MysiRNA-Designer a Software for Rational siRNA Design
Copyright (C) 2011 <M.Mysara et al>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
see the Copyrights files inclosed for this software and other excutables COPYING.
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Requirements
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Windows envirenment
-PPM (Perl Package Manager) varsion (5.10.1.1008):
avaible at (http://www.activestate.com/activeperl/downloads), to be installed.
-Bioperl module follow the "GUI Installation" instructions stated for version 5.10
at (http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows).
After finishing the installation of "Bioperl" install these additional packages:
"bioperl-Run", "Bundle-bioPerl","Modern-Perl" and "spreadsheet-ParseExcel" by
typing their named in the search box of PPM, mark them for install and install them
using the arrow-shaped install icon.
-EMBOSSwin:
available at (http://www.interactive-biosoftware.com/embosswin/embosswin.html).
after installation define a system varriable named "EMBOSSWIN" by accessing windows
"advanced system setting"->"Environment Varriable". Under "system varriables" add
new varriable named "EMBOSSWIN" and give it the PATH where EMBOSSwin is installed.
-Download mRNA dataset (refseq) from NCBI website:(ftp://ftp.ncbi.nih.gov/blast/db/)
named "refseq_rna.tar.gz" extract it using decompressing tools as "winRAR" or "7_Zip".
-WEKA 3.7:
Download and install the software keeping the Path of the installation known to you.
The software is a freeware available online at http://www.cs.waikato.ac.nz/ml/weka/
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Before Running MysiRNA Designer
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-Enable Excel macros by changing the macro security level, Access "Excel Option"->
"Trust Centre"->"Trust Centre Setting"->"Macro settings"->"Enabl all macros".
-Make sure that windows recongized "EMBOSSWIN" varriable by typing one of EMBOSS package
tools as "Cons", check if windows recognize it.
-Access Perl Package Maneger "PPM" installed packages and check if following package are
successfully installed:
"BioPerl","bioperl-Run", "Bundle-bioPerl","Modern-Perl" and "spreadsheet-ParseExcel".
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Running MysiRNA Designer
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-Double click MysiRNA_Designer.exe
-Syntax:
(perl) MysiRNA_Designer.pl -s (file containing accession number(s) with its complete
PATH) -o (path of the output files to be store) -d (path and name of the mRNA refseq
database without its extension) -w Weka installation PATH
- To see the program help type MysiRNA_Designer.pl (with no parameters).
the program will be producing the resutls in a folder name results and the final
results in a folder named total_mysirna
- The program can accept multiple mRNA(s) accession at single run.
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Output Files
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The MysiRNA program generates numerous text output files in varrious folders:
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"tools_results" contains:
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-fasta1results.fasta (Sequence in fasta format of Accession entered),
-fasta1result.gb (Genbank format of the accession entered to be used by get SNPs existence),
-blast1result.fasta (the accession of all the transcripts of the mRNA),
-Tar_acc_result.txt (target accessible siRNA),
-SNPs_free_siRNAs.fasta (siRNA free from SNPs),
-snpsFinal.fasta (SNPs regions),
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"blastresult" contains:
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-siRNA_num_X_Off_Target.fasta (Blast results siRNAs where X change by siRNA number),
-X_Whole_siRNA_off_targets.csv (all the blast results for all siRNA, where X change by
mRNA number).
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"Multi_score_Accepted" contains:
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-X_Multi_score_Approved_siRNA.fasta (siRNA passing multiple scores, multiple transcripts
and SNPs filtration).
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"MysiRNA_Designer_Final_results" contains:
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-X_Final_siRNA.fasta (Final siRNA passing MysiRNA_Designer filtration phases, X changes
with the number of mRNA entered).
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general messages from standard output/error to follow the program stages/errors.
Developed by Mohamed Mysara
if you have any question contact: mm.abdelwahab@nrc.sci.eg, mohamed.mysara@nottingham.ac.uk
and mohamed.abdelwahab@mail.iti.net.eg
