A utility for performing domain architecture-based protein similarity search (using RADS/RAMPAGE).
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README.md

README.md

RadScan

Introduction

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

http://rads.uni-muenster.de

This allows users to run batch-searches etc. Furthermore, RadScan does provides some post-processing options.

RADS

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

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.

System requirements

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.

Usage

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 [150]
    --rads_m <int>                   RADS mismatch penalty [100]
    --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 [0]
    --rampage_t <int>                RAMPAGE gap penalties: Terminal extension [0]

Misc

Authors

The core algorithms and original website were implemented by January Weiner. The rest of the team is:

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

Copyright © 2011-2012 Evolutionary Bioinformatics Group Insitute for Evolution and Biodiversity University of Muenster, Germany

Warranty

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.