3.3 Specifying alphabet indexes
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:
3.3.1 Index1
- None
- If 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.
- User
- A user defined Index1, from a file in the AAIndex1 syntax. The input file is specified using the file={path} argument.
file
3.3.2 Index2
- None
- If 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.
- Diff
- Allow 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].
- User
- A 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.