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siSearch specifications


Unique identifier OMICS_27388
Name siSearch
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Maintained No


Unique identifier OMICS_27388
Name siSearch
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
BioJava, Java Runtime Environment
Maintained No


No version available

Publication for siSearch

siSearch citations


Effective heritable gene knockdown in zebrafish using synthetic microRNAs

Nat Commun
PMCID: 4468906
PMID: 26051838
DOI: 10.1038/ncomms8378
call_split See protocol

[…] Among other tools and websites, we used also GenScript's siRNA Design Center (, siSearch (, IDT SciTools RNAi Design (, Target Finder supplied by Ambion ( […]


Rap1 is indispensable for TRF2 function in etoposide induced DNA damage response in gastric cancer cell line

PMCID: 4491608
PMID: 25821946
DOI: 10.1038/oncsis.2015.1

[…] Two pairs of hairpin siRNA template oligonucleotides for Rap1 based on pSilencer3.1-H1 vector (Ambion, Austin, TX, USA) were designed by siSearch. Oligo-1:5′-GATCCGTGTAGCTCGGAGGATTGAATTCAAGAGATTCAATCCTCCGAGCTACA TTTTTTGGAAA-3′ and 5′-AGCTTTTCCAAAAAATGTAGCTCGGAGGATTGAATCTCTTGAATTCAATCCTCCGAGCTACACG-3′. Oligo-2: 5′-GATCCGTTGGATGTATTTACAG […]


RNAi Screen Indicates Widespread Biological Function for Human Natural Antisense Transcripts

PLoS One
PMCID: 2949395
PMID: 20957177
DOI: 10.1371/journal.pone.0013177

[…] xamined in this study comprise most of the nearly 1,000 sense-antisense transcript pairs, conserved between human and mouse , originally identified through the FANTOM3 transcriptomics effort. We used siSearch to rank all possible siRNAs targeting antisense transcripts of the ∼1000 NAT pairs. We then selected high scoring siRNAs and tested these for specificity, using a wu-blast search against the […]


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siSearch institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
siSearch funding source(s)
Supported by a grant from Pfizer Inc.

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