Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
siDirect Resource Report Resource Website 100+ mentions |
siDirect (RRID:SCR_004853) | service resource, production service resource, analysis service resource, data analysis service | siDirect 2.0 provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5'' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for > 94% of human mRNA sequences in RefSeq. Enter an accession number and retrieve sequence or Paste in a nucleotide sequence. | has parent organization: University of Tokyo; Tokyo; Japan | Special Coordination Fund for Promoting Science and Technology ; Ministry of Education Culture Sports Science and Technology of Japan ; Grant-in-Aid for Scientific Research on Priority Areas 12208003 |
PMID:19948054 PMID:15215364 |
nlx_83672 | SCR_004853 | 2026-07-30 09:27:07 | 243 | |||||||||
|
University of Tokyo; Tokyo; Japan Resource Report Resource Website |
University of Tokyo; Tokyo; Japan (RRID:SCR_011731) | university, institution |
uses: ShareLaTeX is related to: ShareLaTeX is parent organization of: MAboya Gene Expression Patterns and Sequence Tags is parent organization of: 5 prime end Serial Analysis of Gene Expression Database is parent organization of: DBTBS is parent organization of: Full-Malaria: Malaria Full-Length cDNA Database is parent organization of: DBTSS: Database of Transcriptional Start Sites is parent organization of: Autophagy Database is parent organization of: MachiBase is parent organization of: siDirect is parent organization of: U-Compare is parent organization of: FreClu is parent organization of: TogoTV is parent organization of: UT Genome Browser (Medaka) is parent organization of: PoSSuM is parent organization of: MEDIE is parent organization of: Cancer Genomics Project is parent organization of: Comparasite: full length cDNA database is parent organization of: DataBase of Tunicate Gene Regulation is parent organization of: PiSITE: Database of Protein interaction SITEs is parent organization of: SCMD - Saccharomyces cerevisiae Morphological Database is parent organization of: Kinase Pathway Database is parent organization of: Silkworm Genome Database is parent organization of: TRhist is parent organization of: UTGB Toolkit is parent organization of: DROMPA is parent organization of: Japanese Single Nucleotide Polymorphisms is parent organization of: SBM DB is parent organization of: TCC is parent organization of: EBCall is parent organization of: GENIA Project: Mining literature for knowledge in molecular biology is parent organization of: brat rapid annotation tool is parent organization of: KEGG |
SCR_011731 | 2026-07-27 09:33:56 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
