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© Arne Elofsson

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1. Summary

Given the amino acid sequence of a putative alpha-helical transmembrane (TM) protein, TOPCONS predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane. The prediction is a consensus from five different topology prediction algorithms: OCTOPUS, Philius, PolyPhobius, SCAMPI (multiple sequence mode) and SPOCTOPUS . These five predictions are used as input to the TOPCONS Hidden Markov Model (HMM), which gives a consensus prediction for the protein, together with a reliability score based on the agreement of the included methods across the sequence. In addition, the ΔG-scale is used to predict the free energy of membrane insertion for a window of 19 amino acids centered around each position in the sequence. For an explanation of the methods included in the server, see the corresponding links.

The main improvement from the first version of the TOPCONS webserver is that now the server can distinguish between TM and non-TM proteins more efficiently, making it ideal for batch submission of proteins and whole-genome analyses. Further, the server also predicts the presence of potential cleavable signal peptides in the input sequence(s), thus prior scanning with an separate signal peptide predictor is no longer required.

This work used the EGI infrastructure with the support of IN2P3-IRES, INFN-CLOUD-BARI and TR-FC1-ULAKBIM.

2. Usage

Input to the server is an amino acid sequence in FASTA format. The user can either submit paste one or more sequences in the text-area provided, or, alternatively, upload a file for batch submission of sequences. A sequence profile is created for the input sequence using BLAST, and this profile is used as input to all the different methods (except Philius, where only the query sequence is used).

Example input:
>sp|O93740|BACR_HALS4 Bacteriorhodopsin Halobacterium sp.

3. Output

The server outputs the topology predictions using all the individual methods, as well as the consensus prediction (TOPCONS 2.0). In addition, predicted ΔG-values and reliability scores are given for each position in the sequence. The results are both displayed graphically and are available for download in text format in the TOPCONS result file. In the case of batch submission, the results are only presented in raw text format. High-resolution versions of the images are also available for download (single-sequence submission).

The result page of an example job with a single sequence: A job with one sequence
The result page of an example job with multiple sequences: A job with multiple sequences

Please note that the result will be kept on the server for one month and then it will be deleted.

4. Archive policy

The result of finished jobs will be kept on the server for 30 days.

5. References

The TOPCONS web server for combined membrane protein topology and signal peptide prediction.
Tsirigos KD*, Peters C*, Shu N*, Käll L and Elofsson A (2015) Nucleic Acids Research 43 (Webserver issue), W401-W407. [PubMed]
TOPCONS: consensus prediction of membrane protein topology.
Bernsel A*, Viklund H*, Hennerdal A and Elofsson A (2009) Nucleic Acids Research 37 (Webserver issue), W465-8. [PubMed]
OCTOPUS: A method that improves topology prediction for transmembrane proteins by using two-track ANN-based preference scores and an improved topological grammar.
Viklund H and Elofsson A (2008) Bioinformatics. 24, 1662-1668. [Pubmed]
PHILIUS: Transmembrane topology and signal peptide prediction using dynamic bayesian networks.
Reynolds SM, Käll L, Riffle ME, Bilmes JA and Noble WS (2008) PLoS Comput Biol. 11. [Pubmed]
POLYPHOBIUS An HMM posterior decoder for sequence feature prediction that includes homology information.
Käll L, Krogh A and Sonnhammer EL (2005) Bioinformatics. 21, i251-i257. [Pubmed]
SCAMPI: Prediction of membrane-protein topology from first principles.
Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G and Elofsson A (2008) Proc. Natl. Acad. Sci. USA. 105, 7177-7181. [Pubmed]
SPOCTOPUS: SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.
Viklund H, Bernsel A, Skwark M and Elofsson A. (2008) Bioinformatics. 24, 2928-2929. [Pubmed]
ΔG-scale: Molecular code for transmembrane-helix recognition by the Sec61 translocon.
Hessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH and von Heijne G. (2007) Nature 450, 1026-1030. [PubMed]

6. Contact

Arne Elofsson group

Department for Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Sciences
Stockholm University
SE-106 91 Stockholm, Sweden

Science for Life Laboratory
Box 1031, 17121 Solna, Sweden

Phone:   (+46)-8-16 4672
Fax:   (+46)-8-15 3679