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RNAi and SiRNA tools
| Antisense RNA Design aRNA - http://www.idtdna.com/Scitools/Applications/AntiSense/Antisense.aspx/ Antisense RNA Design Tool - [Read more Antisense RNA Design aRNA] |
| BLOCK-iT RNAi Designer - https://rnaidesigner.invitrogen.com/rnaiexpress/ Allows you to design synthetic siRNA, Stealth RNA, or shRNA molecules from nucleotide target sequences, or convert an siRNA molecule sequence into a Stealth?molecule or shRNA molecule. It uses its proprietary algorithm or Tuschl's rules for siRNA design, - [Read more BLOCK-iT RNAi Designer] |
| Gene Link shRNA Design Guidelines Tool - http://www.genelink.com/sirna/shRNAi.asp Gene Link shRNA Design Guidelines Tool. RNAi explorer shRNA design tool - [Read more Gene Link shRNA Design Guidelines Tool] |
| GeneScript SiRNA Target Finder - https://www.genscript.com/ssl-bin/app/rnai GeneScript SiRNA Target Finder - [Read more GeneScript SiRNA Target Finder] |
| Links for SiRNA and Hairpin Tools - http://web.mit.edu/mmcmanus/www/home1.2files/siRNAs.htm Links for SiRNA and Hairpin Tools - [Read more Links for SiRNA and Hairpin Tools] |
| Promega SiRNA Designer Tool - http://www.promega.com/siRNADesigner/program/ Promega SiRNA Designer Tool. This program does not predict hairpins, but the 'split' technology developed by Rossi and colleagues. Like several other programs listed below, a useful aspect of the program is that the user may click on the displayed siRNAs - [Read more Promega SiRNA Designer Tool] |
| pSilencer Converter Ambion - http://www.ambion.com/techlib/misc/psilencer_converter.html This tool generates hairpin siRNA-encoding DNA oligonucleotide inserts from an input siRNA target sequence. The program will add the loop sequence and overhangs for cloning as outlined in the vectors' Instruction Manuals. Ambion - [Read more pSilencer Converter Ambion] |
| RNAi Database for C.Elegans - http://nematoda.bio.nyu.edu/cgi-bin/rnai/index.cgi RNAi Database. This database contains phenotypic data from RNA interference studies in C. elegans. Enter RNAiDB using one of the search options below - [Read more RNAi Database for C.Elegans] |
| RNAi Oligoretriever - http://katahdin.cshl.org:9331/RNAi/html/rnai.html RNAi Oligoretriever. Hannon Lab - [Read more RNAi Oligoretriever] |
| RNAi Phenotypes Wormbase - http://www.wormbase.org/db/searches/rnai_search RNAi Phenotypes Wormbase - [Read more RNAi Phenotypes Wormbase] |
| SciTools RNAi Design Tool - http://www.idtdna.com/Scitools/Applications/RNAi/RNAi.aspx/ SciTools RNAi Design Tool with tutorial. - [Read more SciTools RNAi Design Tool] |
| Silencerâ„¢ Express siRNA Expression Cassette Kits PCR Primer Design Tool - http://www.ambion.com/techlib/misc/SEC_converter.html This tool generates template DNA oligonucleotide sequences from an input siRNA target sequence. Designs for both the "two-oligonucleotide" and "single-oligonucleotide" approach are displayed. These designs are generated using the loop, terminator and RNA - [Read more Silencerâ„¢ Express siRNA Expression Cassette Kits PCR Primer Design Tool] |
| SiRNA at Whitehead - http://jura.wi.mit.edu/bioc/siRNAext/ SiRNA at Whitehead. This site helps you select siRNAs to knock down your gene of interest. After entering your sequence or accession/gi number, choosing pattern for your oligo nucleotides and various filter methods, you will be presented with a list of ol - [Read more SiRNA at Whitehead] |
| SiRNA database - http://www.rnainterference.org/Sequences.html SiRNA database - [Read more SiRNA database] |
| SiRNA Database Compilation - http://web.mit.edu/mmcmanus/www/siRNADB.html SiRNA Database compiled from published sources. - [Read more SiRNA Database Compilation] |
| SiRNA Database Proteinlounge.com - http://www.proteinlounge.com/sirna_home.asp SiRNA Database Proteinlounge.com Very large SiRNA database. 5 day trial. - [Read more SiRNA Database Proteinlounge.com] |
| SiRNA Duplex Finder - http://bioweb.pasteur.fr/seqanal/interfaces/sirna.html SiRNA Duplex Finder. Finds siRNA duplexes in mRNA (EMBOSS) - [Read more SiRNA Duplex Finder] |
| Sirna for SiRNA Design - http://sfold.wadsworth.org/sirna.pl Sirna tool for SiRNA Design. - [Read more Sirna for SiRNA Design] |
| SiRNA Search Ambion - http://www.ambion.com/catalog/sirna_search.php SiRNA Search Ambion - [Read more SiRNA Search Ambion] |
| SiRNA Selector - http://hydra1.wistar.upenn.edu/Projects/siRNA/siRNAindex.htm The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that are specific to the gene of interest. Enter your gene, Gi or accessio - [Read more SiRNA Selector] |
| siRNA Target Finder. Ambion. - http://www.ambion.com/techlib/misc/siRNA_finder.html Find siRNA target sites in your mRNA of interest using the published recommendations of Tuschl and colleagues for siRNA design. Once identified, siRNA targets can be sent directly to one of the kit-specific design tools described below or subjected to a - [Read more siRNA Target Finder. Ambion.] |
| siRNA Template Design Tool - http://www.ambion.com/techlib/misc/silencer_siRNA_template.html siRNA Template Design Tool. for the Silencer® siRNA Construction Kit Ambion. - [Read more siRNA Template Design Tool] |
| SiSearch - http://sonnhammer.cgb.ki.se/siSearch/siSearch_1.7.html siSearch is designed to select siRNAs based on approaches derived from data mining of our siRNA database. We also allow common methods of siRNA design to be included in the search. This includes motif rules, energy conditions and specificity searching. In - [Read more SiSearch] |
| The human siRNA database - http://itb1.biologie.hu-berlin.de/~nebulus/sirna/ The human siRNA database. HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at - [Read more The human siRNA database] |
| The RNAi Consortium shRNA Library - http://www.broad.mit.edu/genome_bio/trc/rnai.html The RNAi Consortium shRNA Library. Short hairpin RNA (shRNA) clones produced by the TRC, as well as protocols for handling and conducting screens with shRNA molecules. The RNAi consortium shRNA library is distributed as bacterial glycerol stocks, plasmid - [Read more The RNAi Consortium shRNA Library] |
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