TopGraph is a membrane topology predictor. it is based on membrane insertion profiles calculated using dsTβL.
What is membrane topology?Plain - the most basic TopGraph run type.
MSA - Multiple Sequence Alignment - a MSA is generated prior to prediction, and improves prediction accuracy considerably. this is the most recommended run type.
TOPCONS - the TOPCONS topology predictor is queried, and the results are used to constrain the TopGraph run.
Constraints - the same as the plain run-type, with user defined constraints. see below.
Constraints MSA - the same as MSA, with user defined constraints. see below
Membrane topology describes the sequence location, length and orientation of transmembranal α-helices. the orientation refers to whether the helix goes from he intracellular to the extracellular or vice versa in the N' to C' direction.
Available run-type options:
TopGraph allows the user to define constraints. constraints should be used whenever external experimental or other data is available, and will improve prediction. possible constraints are:
C terminal - is the protein's C' terminal intracellular or extracellular
N terminal - is the protein's C' terminal intracellular or extracellular
tm position fidelity - allows adding extra positions around all transmembrane positions constrained. if you're not sure about this, don't change the default (0).
TM Pos constraints - segments that will be constrained as transmembranal segments. the user can define the orientation as well
Non TM Pos constraints - regions where no segments will be found.