Two examples of secondary structure assignment by different programs. We chose an averaged NMR structure "1ahk" and a low-resolution X-ray structure (3.0Å) "1fjg" to show as examples since over-prediction by our method is maximum for such structures. Only chain "J" of "1fjg" is shown. Figs. a, b, c show cartoon diagrams of "1ahk", prepared using MOLSCRIPT , for β-strand and α-helix definitions by our program, DSSP  and P-SEA  respectively. β-Strands are shown in yellow and helices in cyan. The N- and C- termini are marked for each structural diagram. The elements produced by our program are labeled. Fig. d shows the secondary structure assignment for "1ahk" by PALSSE (our program), DSSP, P-SEA, DEFINE_S, STRIDE, SSTRUC and PROSS. Our interpretation of β-strands and helices as defined by the different programs are colored in yellow and cyan respectively. The starting positions of each element labeled in fig. a are shown on the first line. The sequence is numbered on the second line with black letters denoting units, red denoting tenths and blue denoting the hundredths places. The protein sequence is shown in the third line. Figs. e, f, g shows cartoon diagrams of chain "J" of "1fjg", prepared using MOLSCRIPT , highlighting β-strand and helix definitions by our program, DSSP, and P-SEA respectively. β-Strands are in yellow and helices are shown in cyan. Elements are labeled in fig. e. Fig. h shows the secondary structure alignment for "J" chain of "1fjg". Definitions produced by the same programs as that used for fig. d are shown. Yellow color is used for our interpretation of β-strands and cyan denotes our interpretation of helices. Green has been used to denote overlaps between helix and β-strand elements defined by our program. The first, second, and third lines show start of each element in fig. e, residue number and sequence respectively, similar to fig d. DSSP, P-SEA, DEFINE_S, SSTRUC, STRIDE and PROSS assignments were generated by obtaining the programs, and then compiling and running them with default parameters on the example PDB files.