Table 2

Known circular permutation results
Protein 1
 Protein 2
 Us
 MASS
 OPAAS
 SAMO
 Topofit
PDB(Length)
 PDB(Length)
 N
 R
 p
 N
 R
 N
 R
 N
 R
 N
 R
1rinA(180)
 2cna_(237)
 152*
 0.875
 10-6
 164*
 1.2
 167*
 1.48
 174*
 1.581
 152*
 1.09
1glh_(214)
 1cpn_(208)
 192*
 1.163
 10-5
 206*
 0.49
 No
 solution
 170*
 3.283
 206*
 0.49
1exg_(110)
 1tul_(102)
 74*
 1.485
 10-4
 60*
 1.9
 No
 solution
 93*
 2.88
 52*
 1.79
1rhgA(145)
 1bcfA(158)
 118*
 1.500
 10-4
 106*
 1.7
 63*
 2.12
 126*
 2.309
 109*
 1.4
1ihwA(52)
 1sso_(62)
 46*
 0.502
 10-3
 39*
 1.7
 No
 solution
 48*
 2.713
 35*
 1.47

Comparison of our alignment results with that of MASS, OPAAS, SAMO, and Topofit for known circular permutations. Each method detected the circular permutations. Our method normally returns more equivalent residues at a lower RMSD. N indicates the number of aligned residues. An * next to the number of aligned residues indicates that a circular permutation was found. R indicates the cRMSD of the alignment. p indicates the p-value of our alignment.

Dundas et al. BMC Bioinformatics 2007 8:388   doi:10.1186/1471-2105-8-388