saRNA Database help page

saRNA database

saRNA is a platform with manually curated database for experimentally validated saRNAs that target various genes involved in cellular processes. saRNA will be useful for people working on RNA biology, epigenetics, differentation etc. and therapeutics based on small RNAs. Besides this platform provides prediction algorithm with model based and design rule based approach. The platform is available free to use at : http://bioinfo.imtech.res.in/manojk/sarna

Browse

Link allows new user to explore the database by any of the given fields categorized in the database as follows:
Condition Studied, Target Gene, Cell_line, study title or Reference ID.

Individual entry details

saRNA-Promoter alignment visuslisation option

Search

Here user can search in two ways:

i) Basic Search:

Input: Enter your query in the box and can specify any of the given fields like sAll fields, Reference (e.g. 20403811), Condition studied (e.g. Apoptosis in human prostate cancer), Target gene (e.g. p21 gene), Experiment used (e.g. Quantitative real time PCR), Cell line used (e.g HeLa), Transfection method used (e.g. lipofectamine), saRNA concentration used (e.g. 50 nM), Time of saRNA treatment (e.g. 72h ). Examples have been provided corresponding to each field, which can be used as sample queries. Besides the option to choose the field, search type allows to retrieve either an exact match or the match containing the query. Clicking on clear data button clears the data after your search.

Output: The results obtained from this search display 6 fields. You can sort the data by clicking on the column header and typing in the boxes given under the headers can do filtering.

Advanced Search

Input: User can built query in the box and can specify any of the given fields like Target gene, concentration ,Time,Transfection method used or else you can keep the default as All option which will search against all the fields in the database.

Output: combination of the queries built using ANd or OR operators can be used e.g. the results obtained from this search display as below.

Tools

i) BLAST:
The BLAST allows alignment of a user provided saRNA sequence against all the sequences available in our database. This helps the user to confirm whether a given sequence or similar one has already been reported or not.

 

ii) Map:
This tool helps you to map database saRNAs on your query or nucleotide sequence. The output of this tool is displayed as showen.

Protein/Biology data exploration
This component deals with the biology and protein machinery and their interacting aprtners as well as their information in external databases.