RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.
BACKGROUND
RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the designing of tools that have minimal off-target effects (i.e. cleaves only the desired sequence). Increasingly, in the current dawn of the post-genomic era, there is a heavy reliance on tools that are suitable for high-throughput functional genomics, consequently more and more bioinformatic software is becoming available. However, to date none have been designed to satisfy the ever-increasing need for the accurate selection of targets for a specific silencing reagent.


RESULTS
In order to overcome this hurdle we have developed RiboSubstrates http://www.riboclub.org/ribosubstrates. This integrated bioinformatic software permits the searching of a cDNA database for all potential substrates for a given ribozyme. This includes the mRNAs that perfectly match the specific requirements of a given ribozyme, as well those including Wobble base pairs and mismatches. The results generated allow rapid selection of sequences suitable as targets for RNA degradation. The current web-based RiboSubstrates version permits the identification of potential gene targets for both SOFA-HDV ribozymes and for hammerhead ribozymes. Moreover, a minimal template for the search of siRNAs is also available. This flexible and reliable tool is easily adaptable for use with any RNA tool (i.e. other ribozymes, deoxyribozymes and antisense), and may use the information present in any cDNA bank.


CONCLUSIONS
RiboSubstrates should become an essential step for all, even including "non-RNA biologists", who endeavor to develop a gene-inactivation system.
Lucier
Jean-François
JF
RNA Group/Groupe ARN, Sherbrooke, Canada. jean-francois.lucier@usherbrooke.ca
Bergeron
Lucien Junior
LJ
Brière
Francis P
FP
Ouellette
Rodney
R
Elela
Sherif Abou
SA
Perreault
Jean-Pierre
JP
D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics; D003698:Hepatitis Delta Virus / Q000201:enzymology / Q000235:genetics*; D006801:Humans; D020407:Internet; D034622:RNA Interference; D016337:RNA, Catalytic / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D013379:Substrate Specificity
D016337:RNA, Catalytic; D012333:RNA, Messenger; D034741:RNA, Small Interfering; C427204:hammerhead ribozyme