Description of DRiPs

DRiPs is a database of periodic repeats in protein sequences built on SwissProt (ver. 51.7). PEPPER tool was used to extract the protein sequences containing tandem repeats and a total of 3142 sequences were found to contain 4713 tandem repeats. A Perl script was used to extract relevant information from SwissProt files containing repeats and the database built in Mysql.

Search Options:
The search box accepts 2 types of queries
• Search by Keyword search, Organism name, SwissProt Id, PDB Id, Repeat Length and Repeat Pattern.
• By combination of the above queries using Boolean (AND, OR, NOT) operators.

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Thus, the format of Search is search option [attribute]. Attributes to be typed capital letters and included inside square brackets only.
The user may also combine two or more attributes using Boolean operators AND, OR, NOT.

Query 1: P02817[SWISSID]

Summary page:

By combination of the attributes used in query 1.

If you want to combine two or more attributes you can use Boolean operators like AND OR NOT
For example if SPID (e.g. P23206) and PDBID (e.g. 1GR3) are known

Query 2:

a) P23206[SPID] AND 1GR3[PDBID]

Summary:

Details:

b) Bos taurus[ORG] OR QPM[PAT]

Summary:

Details:

c) Q28462[SPID] OR NOT 2[RLEN]

Summary:

Details:

3) Multiple uses of Boolean Operators

a) Query 3: P02817[SPID] AND QPL[PAT] AND Bos taurus[ORG]

Summary

Details

b) P02817[SPID] AND QPL[PAT] OR Bos taurus[ORG]

Summary

Details

Search Output Display:
On submitting a query in the search box, a summary page of repeats satisfying the search conditions is generated. The summary page lists the proteins matching the search criteria with a brief description containing Protein Id, Organism name, Description of organism and Repeat Pattern with a hyperlink for details for each result. Upon clicking details link, a new page opens providing detailed information regarding the repeat: Organism name, Taxonomy id, Description, Gene name, Repeat Pattern, Repeat length, Copy number of the repeat pattern, Locus, Start/End positions of the repeat region, Alignment of the repeat pattern with the sequence, SwissProt Id and PDB ID. If the sequence contains same repeat in multiple regions, all the repeats are displayed on the same page.