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Number of citations per year for the bioinformatics software tool DSIR
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Protocols

DSIR specifications

Information


Unique identifier OMICS_04736
Name DSIR
Alternative name Designer of Small Interfering RNA
Interface Web user interface
Restrictions to use None
Input data RNA sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publication for Designer of Small Interfering RNA

DSIR citations

 (27)
library_books

Cis regulatory evolution integrated the Bric à brac transcription factors into a novel fruit fly gene regulatory network

2018
eLife
PMCID: 5752203
PMID: 29297463
DOI: 10.7554/eLife.32273.032

[…] The ORFs for D. melanogaster bab1 and bab2 were obtained from NCBI accession numbers NM_206229 and NM_079155.3 respectively. From these, nucleotide guide sequences were designed using the Designer of Small Interfering RNA (DSIR) algorithm () that is accessible at: http://biodev.extra.cea.fr/DSIR/DSIR.html. For bab1, the eleven rows of output were included in . For bab2, there were 54 r […]

library_books

In retinitis pigmentosa TrkC.T1 dependent vectorial Erk activity upregulates glial TNF α, causing selective neuronal death

2017
PMCID: 5870594
PMID: 29242588
DOI: 10.1038/s41419-017-0074-8

[…] A short hairpin RNA (shRNA) specifically targeting a unique 3′ sequence of the TrkC.T1 mRNA was designed using the DSIR algorithm (http://biodev.cea.fr/DSIR/DSIR.html). The TrkC.T1-targeting shRNA sequence 5′-GGACAATAGAGATCATCTAGT-3′, or a scrambled control sequence 5′-CCTAAGGTTAAGTCGCCCTCG-3′ were cloned into a p […]

library_books

Improved detection of synthetic lethal interactions in Drosophila cells using variable dose analysis (VDA)

2017
Proc Natl Acad Sci U S A
PMCID: 5740648
PMID: 29183982
DOI: 10.1073/pnas.1713362114

[…] ila FDA target libraries. The final FDA library contains 458 Drosophila genes. Two quality amplicons were selected to make the dsRNA library () while three different shRNAs were designed based on the DSIR tool () and were cloned into the Valium20 vector () to make the shRNA library for VDA assays. […]

library_books

Drosophila VAMP7 regulates Wingless intracellular trafficking

2017
PLoS One
PMCID: 5655445
PMID: 29065163
DOI: 10.1371/journal.pone.0186938

[…] To perform RNA interference (RNAi) in the imaginal discs, we generated the shRNA allele of vamp7. The shRNA against vamp7 was designed using DSIR (http://biodev.extra.cea.fr/DSIR/). The top and bottom strands were synthesized, annealed at 95°C for 5 min and cloned into the pWALIUM20 vector as described []. The sequence selected was as foll […]

library_books

Non canonical reader modules of BAZ1A promote recovery from DNA damage

2017
Nat Commun
PMCID: 5636791
PMID: 29021563
DOI: 10.1038/s41467-017-00866-0

[…] blot with anti-BAZ1A (A301-318A, Bethyl Laboratories), anti-BAZ1B (NB600-279, Novus Biologicals), and anti-Tubulin (T9028, Sigma) antibodies. For concurrent depletion of BAZ1B in BAZ1A-KO cells, the DSIR algorithm was used to design a BAZ1B-specific siRNA that was embedded into DNA oligonucleotides and used to generate a shRNA expression cassette in the pINDUCER10 backbone. The targeting sequence […]

library_books

Predicting siRNA efficacy based on multiple selective siRNA representations and their combination at score level

2017
Sci Rep
PMCID: 5357899
PMID: 28317874
DOI: 10.1038/srep44836

[…] er to further exhibit the advantage of our proposed methods, we conduct a serial of comparative experiments among our approaches and the most state-of-the-art systems Biopredsi, ThermoComposition-21, DSIR and i-score both in the classification and regression modes. The 70% threshold of targeted gene knockdown is also used to separate active and inactive siRNAs in Hencken dataset. All models of the […]


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DSIR institution(s)
Centre for Computational Biology, Ecole des Mines de Paris, Fontainebleau, France; Laboratoire de Biologie, Informatique, Mathématiques, Département Réponse et Dynamique Cellulaire, CEA Grenoble, Grenoble, France
DSIR funding source(s)
This work was supported in part by the Cartes d'Identité des Tumeurs (CIT) program of the Ligue Nationale Contre le Cancer.

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