ASPsiRNA

FAQs

Q1. What is ASPsiRNA?

ASPsiRNA is a comprehensive repository of a new category of therapeutically relevant siRNAs called Allele specific siRNAs (ASP-siRNAs), which can differentiate between two alleles of a target gene even with one single nucleotide difference.

It is the only database of ASP-siRNAs involved in human hereditary disorders. Currently, our archive contains a total of 4543 ASP-siRNAs targeting 78 unique genes involved in 51 different human genetic diseases.

Q2. How Allele discriminative-siRNAs are different from indiscriminate siRNAs?

Traditional siRNAs are effective and specific to target a particular target gene, but they are not usually effective to discriminate target sequence from non-target ones with single nucleotide difference. Therefore they use to suppress both targets with equal efficacy, while ASP-siRNAs are designed in such a way that it can discriminate the mutant gene from the wild type gene counterpart. This high level of specificity and efficacy is observed in these siRNAs in recent scientific literature.

Q3. What is the implication of ASPsiRNA database to scientific community?

Since, ASP-siRNAs have potential to discriminate the wild and mutant allele of a single gene, this would be amenable for the treatment of those hereditary disorders in which wild type allele is critical for organismÕs survival. Therefore in order to look for a better therapeutic for these type of diseases; it should ideally do not harm wild-type allele, ASP-siRNAs stands very well to combat and cure these disease in a better way.

Therefore, to make these ASP-siRNAs quickly accessible in the form of a centralized, comprehensive database; we have developed ASPsiRNA. There are two implications of this archive:

a)   To keep updated experimentally validated ASP-siRNAs/shRNAs reported in scientific literature at one stand-alone database.

b)   This database will be beneficial to develop an Algorithm for the designing highly effective ASP-siRNAs and might also provide guide to increase the specificity of siRNAs by machine learning techniques.

Q4. What are the fields of ASPsiRNA?

These are as follows-

(1) PMID, (2) ASPsiRNA ID, (3) ASPsiRNA name, (4) ASPsiRNA sequence, (5) mutant allele sequence, (6) ASPsiRNA efficacy for mutant allele, (7) ASPsiRNA efficacy for wild allele, (8) Percentage discrimination,(9) mismatch position ,(10) wild siRNA ,(11) wild allele ,(12) wtsiRNA efficacy for wild allele, (13) wild siRNA efficacy for mutant allele, (14) Percentage discrimination, (15) mismatch in,(16) concentration, (17) Target gene name, (18) UniProt ID ,(19) target sequence, (20) GenBank, (21) mutation in target gene, (22) RefSNP, (23) cell line, (24) technique, (25) expression method ,(26) transfection method, (27) transfection duration, (28) disease, (29) OMIM ID, (30) KEGG disease ID, (31) HUGO ID, (32) clinical significance of mutation, (33) Delivery method, (34) title of the article/patent,(35) Authors, (36) Reference, (37) target position, (38) mutation at gene level, (39) cytogenic location of the gene, (40) genomic coordinates, (41) mutation/variant category, (42) ClinVar ID.

Q5. How to use search option in ASPsiRNA?

User can perform search option in the following two ways:

1. User can perform a quick search by giving a keyword to the Òquick searchÓ radio button provided at the top of the web interface and click submit.

2. Second, user can enter the query/keyword after clicking search on menu bar. User given keyword can be searched in the any of the 16 representative fields of the entire database categorized in three parts:
a) ASPsiRNA details like ASP-siRNA ID, ASP-siRNA name, its antisense sequence, mismatch in siRNA, ASP-siRNA percentage efficacy against mutant allele, percentage discrimination.

 b) Target gene/disease details like target gene, target mutation, mutation category/variant, SNP, disease and pathogenic status of mutation pertaining to that disease. 

c) Important Experimental details like cell line, experimental technique used to determine efficacy/expression of ASP-siRNAs like dual luciferase reporter assay, PMID, Author.

There is also facility that user can select some out of all fields to search that keyword in those fields only.

Q6. Describe the tools incorporated in ASPsiRNA and their advantage?

We have provided three tools in ASPsiRNA to help user analyze their sequence. These are:

1) ASPsiBLAST 2) ASPsiOffTar (seed-based) 3) ASPsiOffTar (full sequence-based) and 4) ASPsiMAP tool

Q7. What is the use of ASPsiBLAST tool?

The ASPsiBLAST tool searches the ASP-siRNA sequence in the archive similar to the siRNA sequence provided by the user and searches whether that siRNA sequence have been already reported in the literature or not.

Q8. What is the use of ASPsiAlign tool?

ASPsiAlign aligns the user given siRNA sequence on the human reference genome.

Q9. What is the use of ASPsiRNA Map tool?

This tool can be use to map the ASP-siRNAs in the database against the user given target gene sequence. Therefore it can be helpful to use these siRNAs for the suppression of desired target gene sequence.

Q10. How to download data from ASPsiRNA?

Data is freely available to download from ASPsiRNA under the download section in the menu bar. User can download either Allele specific siRNAs; also entire database can also be downloaded depending upon their requirement.

Q11. How to submit data in ASPsiRNA?

Experimental biologists, who are doing research in the field of are welcomed to submit their experimentally validated ASP-siRNA sequences in the database.

Q12. Is this database freely available?

Yes, this database is freely available through this URL: http://crdd.osdd.net/servers/aspsirna