RASPODOM

RASPODOM is a program to detect circular permutations (CPs) using an efficient dynamic programming algorithm.

Features:

fast searching for CPs by comparing all sequences within a file
output of the Needleman-Wunsch matrix as EPS

The current version can be found here: raspodom.tar.gz

Installation

 tar xfz raspodom.tar.gz
 cd raspodom
 make

Usage

The input file should be in XDOM format. An example of a file with two sequences, each consisting of 5 domains is shown below:

Future

We are currently developing a new version of RASPODOM. We are planning for it to have the following features:

compare all sequences within a file
search for CPs in a sequence file providing a query arrangement

Background

Circular permutations (CPs) are changes in domain arrangements so that a N-terminal fragment of a protein is transferred to the C-terminus (e.g. ABCD → CDAB). A possible mechanism explaining the formation of CPs is a multi step process (see Figure). Initially, a duplication of a protein leads to a protein with an arrangement repeat. Subsequently, terminal domains at the C- and N-terminus are lost reducing the protein to the original number of domains, but in a different order.

Circular permutations can be a result of an initial duplication and subsequent loss of terminal protein domains.

Citation

If you used RASPODOM in your project please cite our publication:

Weiner J 3rd, Thomas G, Bornberg-Bauer E, Rapid motif-based prediction of circular permutations in multi-domain proteins, Bioinformatics. 2005 Apr 1;21(7):932-7. doi:10.1093/bioinformatics/bti085

https://academic.oup.com/bioinformatics/article/21/7/932/268835