Some methods require an "alphabet index" to be specified. Alphabet indexes associate a value with each alphabet state (Index1, e.g. a biochemical property) or for a pair of states (Index2, e.g. a biochemical distance). This section describes the supported indexes:
NoneIf no index should be used.
Surface, Mass, Volume, Charge {AA}Basic amino acids properties.
GranthamPolarity, GranthamVolume {AA}Grantham’s polarity and volume index.
KleinCharge {AA}Klein’s charge.
ChouFasmanAHelix, ChouFasmanBSheet, ChouFasmanTurn {AA}Chou and Fasmani score for secondary structure prediction.
ChenGuHuangHydrophobicity {AA}Hydrophobicity according to Chen, Gu and Huang.
SEALow, SEAMedium, SEAHigh {AA}Solvent Exposed Area, percent of amino acids having a SEA below 10, between 10 and 30, or higher than 30, respectively.
UserA user defined Index1, from a file in the AAIndex1 syntax. The input
file is specified using the file={path} argument.
file
NoneIf no index should be used.
Blosum50 {AA}The BLOSUM 50 amino acid distance matrix.
Grantham, Miyata {AA}Two biochemical distance matrices. Both accept an optional argument
symmetrical={boolean} allowing to specify if the matrix
should be symmetric or not. If not, the distance measure will be
signed.
DiffAllow to compute a distance matrix by taking the difference for, each
pair of state, of an Index1 value. The Index1 to use is specified
using the index1={Index1 description} argument. An
additional argument allow to specify whether the resulting matrix
should be symetric (symmetrical={boolean}): if so, the
absolute difference will be used. Alternatively, the distance will be
signed and d[i,j] = - d[j,i].
UserA user defined Index2, from a file in the AAIndex2 syntax. The input
file is specified using the file={path} argument. The
symmetrical={boolean} argument can be used to specify
whether distances should be signed or not.