siRNA DNA Designer
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Version 1.5 of siRNA DNA Designer has been released. The following features have been added.
1) BLAST Engine:
A BLAST Engine is now included with siRNA DNA Designer 1.5 which permits desktop analysis for potential off-target hits.The Blast engine performs a search for off-target hits using the set of obtained siRNA candidate sequences as the query against the refseq RNA database. There are two advantages over most BLAST servers. First, most BLAST servers use the entire nr nucleic sequences database which contains non-coding sequences in great excess over coding sequences. Hits against the non-coding sequences are irrelevant to siRNA effects and obscure the analysis. By using only the refseq RNA data base, only relevant sequences are considered. Secondly, the siRNA DNA Designer 1.5 BLAST engine performs an RNA to RNA alignment, which accounts for the occurrence of G:U wobble pairs. This again provides a more relevant search for off-target interactions with other mRNA sequences than a DNA to DNA BLAST. The BLAST window has simple step by step instructions.
2) Support for the Epicentre MessageMuter™ shRNAi Production Kit
The Epicentre tab has pre-set parameters and a step by step tabbed pane for designing oligos for the MessageMuter™ shRNAi Production Kit from Epicentre, Inc.. This kit produces shRNA by in vitro transcription, thereby simplifying the production of RNAi compared to in vitro transcription to produce separate RNA strands which must be annealed.
The download for the trial version is:
www.irisgenetics.com/Web_Installers/install.htm
For windows, and Linux be sure to install the free java VM download if you hav not already done so.
Java easy install http://java.com/en/index.jsp
For Apple computers, version 1.5 of siRNA DNA Designer requires the Panther edition of OSX(10.3 or higher). The java version 1.4.2 is required also. It is preinstalled on most versions of the Panther edition. If not, it may be downloaded from Apple with software update in the System Preferences window.
1) BLAST Engine:
A BLAST Engine is now included with siRNA DNA Designer 1.5 which permits desktop analysis for potential off-target hits.The Blast engine performs a search for off-target hits using the set of obtained siRNA candidate sequences as the query against the refseq RNA database. There are two advantages over most BLAST servers. First, most BLAST servers use the entire nr nucleic sequences database which contains non-coding sequences in great excess over coding sequences. Hits against the non-coding sequences are irrelevant to siRNA effects and obscure the analysis. By using only the refseq RNA data base, only relevant sequences are considered. Secondly, the siRNA DNA Designer 1.5 BLAST engine performs an RNA to RNA alignment, which accounts for the occurrence of G:U wobble pairs. This again provides a more relevant search for off-target interactions with other mRNA sequences than a DNA to DNA BLAST. The BLAST window has simple step by step instructions.
2) Support for the Epicentre MessageMuter™ shRNAi Production Kit
The Epicentre tab has pre-set parameters and a step by step tabbed pane for designing oligos for the MessageMuter™ shRNAi Production Kit from Epicentre, Inc.. This kit produces shRNA by in vitro transcription, thereby simplifying the production of RNAi compared to in vitro transcription to produce separate RNA strands which must be annealed.
The download for the trial version is:
www.irisgenetics.com/Web_Installers/install.htm
For windows, and Linux be sure to install the free java VM download if you hav not already done so.
Java easy install http://java.com/en/index.jsp
For Apple computers, version 1.5 of siRNA DNA Designer requires the Panther edition of OSX(10.3 or higher). The java version 1.4.2 is required also. It is preinstalled on most versions of the Panther edition. If not, it may be downloaded from Apple with software update in the System Preferences window.
