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Table 1 Amino acid encoding.

From: IgTM: An algorithm to predict transmembrane domains and topology in proteins

Amino acid

Property

Dayhoff

C

sulfur polymerization

a

G, S, T, A, P

small

b

D, E, N, Q

acid and amide

c

R, H, K,

basic

d

L, V, M, I

hydrofobic

e

Y, F, W

aromaticity

f

  1. The Dayhoff encoding takes into account the properties of each residue: sulfur polymerization, small, acid and amide, basic, hydrophobic and aromaticity. For example, for the input protein segment SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRV the output encoded sequence would be: beeeccbeebeefcbfcbdedbbcbebcdebede
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BMC Bioinformatics

ISSN: 1471-2105

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