[This is a review of the original version - see Text S1 for the version history]

This page describes circularly permuted proteins and for the most part is a good starting point for this subject. However, I have several comments.

The first line reads "Circular permutation is a process during evolution <http://en.wikipedia.org/w...> that changes..." I think strictly speaking it isn't an evolutionary process, but a description of the relationship between proteins that sometimes is a clear evolutionary process (sometimes a post-translational one, which I get-it is also evolutionary in some sense; at other times they are engineered as the author points out). The first permutation (concanavalin A) is more of a functional modification. I think a better opener would be to speak of it as a relationship between proteins. in other words, "Circular permutation in proteins describes the situation where one protein is circularly permuted relative to another related protein." (and then ellaborate on the other points)

I would perhaps mention that the post-translational modification of concanavalin A is a cleavage and an unusual protein-ligation (there are, I presume, suitable cross-references here too).

Re: the Swaposin story, Russell has two Ls, and I would avoid the non-wikipedia subjectivity statements like "lighthearted" - I would just say nicknamed. These are the kinds of things that get flagged in Wikipedia - the stuff has to read like an encyclopedia and not an editorial.

Re: Programmatic detection. I think this English is a bit dubious and perhaps the section would be more appropriately headed "Detection of Circular Permuations" (or similar). This section could also do with some slightly longer introduction about why it is problematic to detect these using standard techniques like dynamic programming, etc. And one reference in this list is missing which I believe to be the first method to detect permutations: Michael Zuker, JMB 221:403-420, 1991 Suboptimal sequence alignment in molecular biology: Alignment with error analysis.

The figure showing Concanavalin A and Lectin is a little hard to understand - it might be easier to use a two color (N- and C- terminus) rather than a color ramp, but perhaps this won't help - worth trying perhaps.