Topcons 2.0 / TOPCONS-single – Consensus Prediction of Membrane Protein Topology / without BLAST runs

Topcons 2.0 /  TOPCONS-single


TOPCONS  is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by approximately 10 percentage points.


TOPCONS-single is a consensus method for topology prediction of alpha-helical membrane proteins, but without the need for BLAST runs. It is based on several tools that accept a single protein sequence as input (S-TMHMM, HMMTOP, MEMSAT, PHOBIUS and TopPred). Ideal for a quick scan of entire genomes.


Stockholm Bioinformatics Center




  • Linux/MacOsX/Windows
  • cmake.


  Topcons /  TOPCONS-single



Bernsel A, Viklund H, Hennerdal A, Elofsson A. (2009)
TOPCONS: consensus prediction of membrane protein topology.
Nucleic Acids Research 37(Webserver issue), W465-8

Bioinformatics. 2011 May 1;27(9):1322-3. doi: 10.1093/bioinformatics/btr119.
Rapid membrane protein topology prediction.
Hennerdal A1, Elofsson A.

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