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Help Page of BOSS Database


Search
Advance Search
Data architecture
Browse
Tools
DESCRIPTION
FAQs
Main Page
BOSS database, will provide the comprehensive details of the experimentally validated breast cancer specific breast cancer genes at one platform, to help researchers working in the field of siRNA based anticancer therapeutic development.

Simple Search

This search option is the simplest way to search BOSS DB. This Search tool provide us for searching all seventeen fields or on selected fields of database and users are free to display all or selected fields.

Advance Search

This option allows users to perform advance search by making many combinations.The advance search provides us the best way to search database using several combinations of keywords of fields using logical operators “AND & OR” to make advance query for getting more refined results. The keyword should be without spaces.



Data architecture
This BOSS DB contains the following seventeen fields for each siRNAs entry; (1) BOSS id (2) pubmed id, (3) sequence, (4) siRNA name, (5) target gene, (6) GC content, (7) Length of siRNA, (8) cell types, (9) year, (10) siRNA source (siRNA/shRNA), (11) Position of siRNA , (12) Test objective, (13) Test method, (14) NCBI Acession no., (15) Biological inhibition, (16) Transfection Reagent and (17).


BROWSING OPTIONS


Browse
We have designed powerful browsing facility tools that allows a user to browse data using various options. A short description of web interfaces designed for browsing are as follows: This option allows user to browse BOSS DB based upon some main categories like siRNA Name, Target Gene, Cell Type, Inhibition, GC Content and Test Time of breast oncogenic specific siRNAs. User can select any of the category and click button. A list of breast oncogenic specific siRNA related to category will be displayed We have designed powerful browsing facility tools that allows a user to browse data using various options. A short description of web interfaces designed for browsing are as follows: This option allows user to browse BOSS DB based upon some main categories like siRNA Name, Target Gene, Cell Type, Inhibition, GC Content and Test Time of breast oncogenic specific siRNAs. User can select any of the category and click button. A list of breast oncogenic specific siRNA related to category will be displayed


TOOLS


BOSS database blast
User can use this tool for similarity-based search of any query sequences with those present in BOSS database. By doing this, user can confirm whether a given siRNA sequence or similar siRNA sequence has already been reported or not? User can submit query sequence in single FASTA format in search field and press the submit button. It will display all siRNAs similar to query sequence. The server provides option to modify different parameters like scoring matrices, gap penalty, word size etc.

siRNAmap
The siRNAMAP maps the BOSS DB siRNA's on the user nucleotide sequence . It will be provide the list of siRNA from BOSS DB which are complementary to the user provided sequences.


DESCRIPTION OF FIELDS


1.ID: Each BOSS siRNA sequence has been assigned a unique ID.

2. PubMed ID: All the information regarding a particular breast oncogenic specific siRNAs has been taken from published literature. PMID is a unique identifier assigned to each article as it is added to PubMed.

3.BOSS sequence: It represents the sequence of BOSS DB taken from the published literature.

4. siRNA Name: It is the name assigned to a particular breast oncogenic siRNA in literature.

5.siRNA Source: It represents the siRNA Source of BOSS DB whether it can be siRNA OR shRNA sequences

6.Target Gene: It represents the target site sequence on particular breast oncogenic gene, it means siRNA against that target gene etc.

7.GC Content: Guanine-Cytosine content (GC-content) is the percentage of nitrogenous bases on a breast oncogenic specific siRNAs molecule that are either guanine or cytosine. GC-content is the tool for visualizing and analyzing the variation of GC content in genomic sequences (CT et.al, 2006).

8.Test Objective: Activity of siRNA
Unknown: no information found regarding the N-terminal modifications.

9.Test method: Assay were used in test method

10.Position of siRNA: Start Postion of siRNA in genomic sequences.

11.Inhibition value: Biological inhibition value of breast oncogenic specific siRNAs.

12.Transfection Reagent: Transfection Reagent is a novel, nonliposomal formulation designed to transfect DNA into a wide variety of cell lines with high efficiency and low toxicity (Promega).

13.Length of siRNA: Total length of siRNA in BOSS DB .

14.Cell type: Types of breast cancer cell lines used in this database.

15.Test Time: Total test time used in experiment .

16.NCBI Accession: A sequence version number consists of a base Accession number, a dot, and a version suffix that starts with 11. (This identifier is often referred to as an "accession dot version".) The base Accession number identifies the sequence record, and the version suffixes form the series of versions, starting with 11. A sequence Accession number without a version suffix always refers to the latest version of the sequence.(Gene bank ).

17.Year: Year of publications.


NA: when no dataset has been assigned.


FREQUENTLY ASKED QUESTIONS


Below are commonly asked questions. If you can not find the answer to your question or have a suggestion please go to the Contact


Q1. What is BOSS DB?
Ans. BOSS Database is a collection of experimentally validated breast oncogenic specific siRNAs reported in the literature.

Q2. Why CPPsite is created?
Ans.BOSS Database is one of the most promising tools for experimentally validated breast oncogenic specific siRNAs., It will be huge therapeutic potential for breast cancer. To the best of our knowledge, in spite of wealth of information on breast oncogenic specific siRNAs, no such database exists at present. Therefore, to help researchers who are working in the field of siRNAs based drug discovery, we have developed a comprehensive database which provides all the basic information about siRNAs.

Q3. What is unique about BOSS DB?
Ans. BOSS DB is a first and unique database of its kind, which has many online webtools. One of the powerful tools is siRNA mapping and Blast search,in which siRNA mapping provide the list of siRNA from BOSS DB which are complementary to the user provided sequences while in Blast search user can use this tool for similarity-based search of any query sequences with those present in BOSS DB. By doing this, user can confirm whether a given breast oncogenic specific siRNA sequence or similar .

Q4. Does this database represent all experimentally validated siRNAs?
Ans.Yes this database represent all experimentally validated siRNAs from scientific literture?.

Q5.Why search BOSS DB?
Ans. BOSS DB provides all experimental information of used siRNAs such as Sequence, siRNA Name, Target Gene, GC Content,Test Objective and cell lines used etc. This information will be very useful for researchers working in breast cancer.

Q6. How do I process a text search with BOSS DB?
Ans: You can process any Length of siRNA, or id search through the BOSS DB IN search or you may go to ADVANCE search for specific keyword.

Q7. To whom can I report a discrepancy?
Ans. Please refer to the "Contact" page.

Q8. Is this database freely available?
Ans. This open source project is freely available through this Contact

 

Biotechnology Division, Central Institute of Medicinal and Aromatic Plants Lucknow, India