RadScan is a command line utility for performing domain achitecture-based similarity searches against UniProt. It interfaces a webapplication which runs a reference implementation of the RADS/RAMPAGE based search. As such, RadScan does not implement either RADS or RAMPAGE - it provides access to the webapplication of RADS running under
This allows users to run batch-searches etc. Furthermore, RadScan does provides some post-processing options.
RADS stands for __R__apid __A__lignment of __D__omain __S__trings. As the name suggests, RADS beforms a Needleman-Wunsch-like alignment on Domain String. Using a classical dynamic programming scheme, RADS returns a score representing the similarity of domain architectures (and is very swift in doing so).
RAMPAGE is a upplement to RADS, and perform a NW sequence alignment on similarity block obtained from the RADS search.
Please note: we are currently in the process of publishing RADS/RAMPAGE, and will keep it vague here until that is done (besides a couple of words below). If you want to know more about RADS/RAMPAGE, get in touch with us.
RadScan is written in Java and requires Java 6.0 or higher. We have tested it on *unix-based systems. In principle, it should run on other operating systems with a Java virtual machine. Get in touch if you encounter any problems.
RadScan is run from the command line. It accepts xdom, fasta and raw-sequence format as input. Sequence data (amino acids) is required to run RadScan in RAMPAGE mode.
The XDOM format
The xdom format is a simple, domain-centric, fasta-like representation of proteins. For example, the Human ATP-binding cassette sub-family F member 2 (Q9UG63) contains three Pfam-A domains:
>Q9UG63 623 44 257 ABC_tran 296 383 ABC_tran_2 437 545 ABC_tran
The first line specifies the protein ID and its length in amino acids. The remaining lines specify each domain (in sequence) with its repective co-ordinates and ID or accession number. Optionally, the ID fields can be followed by an Evalue inidcating the significance of the hit between the domain sequence and the defining model.
$ java -jar radscan.jar -h
Usage: radscan [OPTIONS] -in <query> Rapid Alignment Domain Search - find proteins with similar architectures -a,--algorithm <name> Search algorithm to run. Currently supports RADS or RAMPGAE. [Default: RADS] -h,--help Show this help -I,--ID-only Only return ID of hits (list) -i,--infile <file> Query: protein in XDOM or FASTA format -m,--matrix <substitution matrix> Amino acid substitution matrix (used in RAMPAGE mode) [Default BLOSSUM62]. See ftp://ftp.ncbi.nih.gov/blast/matrices/ for a list of supported matrices -max,--maxHits <int> Limit maximum number of results (top x) -o,--out <file> Outfile for results (xdom) -q,--quiet Quiet mode - surpress all output except for results (incl. score table) --rads_g <int> RADS gap penalties: Internal extension [-25] --rads_G <int> RADS gap penalties: Internal opening [-50] --rads_M <int> RADS match score  --rads_m <int> RADS mismatch penalty  --rads_t <int> RADS gap penalties: Terminal extension [-50] --rads_T <int> RADS gap penalties: Terminal opening [-100] --rampage_g <int> RAMPAGE gap penalties: Internal extension [-1] --rampage_G <int> RAMPAGE gap penalties: Internal opening [-10] --rampage_T <int> RAMPAGE gap penalties: Terminal opening  --rampage_t <int> RAMPAGE gap penalties: Terminal extension 
The core algorithms and original website were implemented by January Weiner. The rest of the team is:
- Erich Bornberg-Bauer (email@example.com)
- Sonja Gath (firstname.lastname@example.org)
- Andrew D. Moore (email@example.com)
- Nicolas Terrapon (firstname.lastname@example.org)
How do I reference?
As previously mentioned, this is very much work in progress (we are currently working on a publication describing RADS/RAMPAGE). Until then, please contact us before using RADS/RAMPAGE in your work.
Copyright © 2011-2012 Evolutionary Bioinformatics Group Insitute for Evolution and Biodiversity University of Muenster, Germany
This software is provided “as is” and without any express or implied warranties, including, without limitation, the implied warranties of merchantibility and fitness for a particular purpose.