Options

Sequence weighting method🤔2 types of sequence weighting method to reduce redundancy in an input MSA are implemented in this program, the Position-Based method by Henikoff-Henikoff and the Distance-Based method by Vingron-Argos. : Position-Based Distance-Based

Window size🤔By setting this window, incorporating sequential neighboring sites can be taken into account among the conservation scores.

[e.g.] If the window size is 3, a set of 3 conservation scores on either side of site n (n-3, n-2, n-1, n+1, n+2 and n+3) are taken into account as moving average. : 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Tolerate non-standard residues🤔If Yes, the program tolerates non-standard residues such as 'B', 'Z' and 'X' etc. in an input dataset by converting them into gap symbols.

If No, the program halts anyway if an input dataset includes these non-standard residues. : Yes No

Colorize the residues🤔If Yes, residues in each site are colorized based on their 6 types of sterochemical propaty as follows:

Aliphatic ( A, V, L, I, M, C )

Aromatic ( F, W, Y, H )

Polar ( S, T, N, Q )

Positive ( K, R )

Negative ( D, E )

Special conformations ( G, P )
: Yes No

Colorize the scores🤔Make the conservation scores have a color gradient in response to their values as follows:

Thermo : ■■■■■■
Ocean : ■■■■■■
Flame : ■■■■■■
Neon : ■■■■■■
V a p o r W a v e : ■■■■■■ : None Thermo Ocean Flame Neon V a p o r W a v e