Table 1. Algorithms for comparing pairs of circularly permuted proteins.

Name	Type	Description	Author	Year	Availability	Reference
FBPLOT	Sequence	Draws dot plots of suboptimal sequence alignments.	Zuker	1991		[34]
Bachar et al.	Structure, topology independent	Uses geometric hashing for the topology independent comparison of proteins.	Bachar et al.	1993		[35]
Uliel at al.	Sequence	First suggestion of how a sequence comparison algorithm for the detection of circular permutations can work.	Uliel et al.	1999		[36]
SHEBA	Structure	Duplicates a sequence in the middle; uses SHEBA algorithm for structure alignment; determines new cut position after structure alignment.	Jung, Lee	2001		[37]
Multiprot	Structure, topology independent	Calculates a sequence order independent multiple protein structure alignment.	Shatsky	2004	Server, download	[38]
RASPODOM	Sequence	Modified Needleman and Wunsch sequence comparison algorithm	Weiner et al.	2005	Server	[39]
CPSARST	Structure	Describes protein structures as one-dimensional text strings by using a Ramachandran sequential transformation (RST) algorithm. Detects circular permutations through a duplication of the sequence representation and “double filter-and-refine” strategy.	Lo, Lyu	2008	Server	[40]
GANGSTA+	Structure	Works in two stages: Stage one identifies coarse alignments based on secondary structure elements. Stage two refines the alignment on residue level and extends into loop regions.	Schmidt-Goenner et al.	2009	Server, download	[41]
SANA	Structure	Detect initial aligned fragment pairs (AFPs). Build network of possible AFPs. Use random-mate algorithm to connect components to a graph.	Wang et al.	2010	Download	[42]
CE-CP	Structure	Built on top of the combinatorial extension algorithm. Duplicates atoms before alignment, truncates results after alignment.	Bliven et al.	2010	Server, download	[43]