Please note: This webapplication is a proof-of-concept of the RADS-RAMPAGE algorithms (publication in Bioinfomatics in January 2014). When using it, please keep in mind that it is still under construction.
Batch searches: For running RADS/RAMPAGE searches in batch mode, we provide a command-line program which queries the web interface. It can be downloaded here (requires Java).
User id 1464442444-9161
[ Move your mouse over the little yellow buttons to get context help ]
RADS is a program to detect homology of proteins by comparing the domain arrangements of proteins.
In RADS, amino acid sequences are not directly compared between your query and the proteins in the database
(here, Simap that gather proteins from PDB, Uniprot, RefSeq and Genbank). Instead, RADS examines the protein domains (from Pfam database) present in the protein and looks up in our local database which proteins
have a similar arrangement of domains.
This approach has two major advantages.
Finally, using RADS along with BLAST, allows you to find functional homologs that have an identical (or similar) domain arrangement, but little sequence conservation.
To identify such case, you could look for the
hits with low BLAST score (or those which were not detected by BLAST), but having a high RADS score.
RADS needs only information about domains, RAMPAGE also needs information about a sequence. Both are happy with just an identifier from the database used.