RBSDesigner software was published in Bioinformatics (click).
RBSDesigner was developed to computationally design synthetic ribosome binding sites (RBS) to control gene expression levels. Generally transcription processes are the major target for gene expression control, however, without considering translation processes the control could lead to unexpected expression results since translation efficiency is highly affected by nucleotide sequences nearby RBS such as coding sequences leading to distortion of RBS secondary structure. Such problems obscure the intuitive design of RBS nucleotides with a desired level of protein expression. We developed RBSDesigner based on a mathematical model on translation initiation (see here) to design synthetic ribosome binding sites that yield a desired level of expression of user-specified coding sequences.
The latest stable version of RBSDesigner is 1.0.78
Please read followings for installation before downloading RBSDesigner !!!
1. Install UNAFold
RBSDesigner requires UNAFold to predict RNA secondary structures and has been tested to work with UNAFold 3.6.
!!! The recent version of UNAFold (3.8) is not compatible with RBSDesigner. You can download UNAFold 3.6 here. We are working to solve the compatibility issue. The recent UNAFold can be downloaded at http://dinamelt.bioinfo.rpi.edu/download.php.
2. Install Perl
UNAFold requires Perl to be installed. If you already installed Perl, skip this step. Otherwise, download Perl and install. We recommend downloading and installing ActivePerl (you can download ActivePerl from this site or its distributor’s site).
3. Install RBSDesigner
To download RBSDesigner, click here. RBSDesigner will install files where UNAFold executable files are (C:\Program Files\UNAFold\bin).
4. We recommend checking whether Perl and UNAFold are properly working or not. Run RBSDesigner and press the “Check UNAFold and Perl” button which pops up a window (see below). Then, press “Check Perl” and “Check UNAFold“. If you see the help screen of both Perl and UNAFold, the programs are successfully installed and ready to run RBSDesigner. Otherwise, you need to check whether Perl and UNAFold are properly installed.
5. For the compatibility issue of Windows Vista or 7, if necessary, please set the compatibility of “RBSDesigner.exe” to Windows XP.
For any bug reports or inquiries, please send an email to dna at ssbio.cau.ac.kr