TOPCONS-single Sunday, July 14 2024
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About TOPCONS-single
Pre-run predictions for whole genomes


1. Summary

Given the amino acid sequence of a putative alpha-helical membrane protein, TOPCONS-single predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane. TOPCONS-single uses the TOPCONS algorithm to give a consensus prediction of the topology. As input, six different topology prediction methods that do not use any homlogy information, i.e. does not require BLAST, are used.

Note that the server does not predict cleavable signal peptides, which are easily confused with TM segments. If signal peptides are likely to be present in the input data, a separate signal peptide predictor such as SignalP should first be applied and predicted signal peptides cleaved off before submitting the sequence to TOPCONS-single.

2. Usage

This server is appropriate for topology predictions of large protein datasets. Input to the server is amino acid sequences in FASTA format. Using the text window, the maximum number of sequences per query is 1,000, and using the file upload option, the maximum number of sequences per query is 100000. If you only have one or a few sequences, use the TOPCONS server instead.

3. Output

The server outputs prediction results in a number of text files:

Predicted topologies: Text file containing the predicted topologies for all proteins in a FASTA-like format, where i=inside (cytoplasmic side), M=membrane and o=outside (extra-cytoplasmic side).

List of predicted TM proteins: A list containing the names of all proteins with at least one predicted TM region.

List of predicted non-TM proteins: A list containing the names of all proteins with no predicted TM regions.

Reliability scores:Each prediction is assigned a score ranging from 1 to 100, reflecting how certain the prediction can be considered to be. One or more submethods giving similar predictions typically gives a high reliability score.

Topologies from submethods: Text file containing the predicted topologies from the submethods for all proteins in the format described above.

Error reports: If for some reason a submethod fails on a particular protein, the protein and the method are listed in this file. TOPCONS-single still produces a prediction in such cases, it just doesn't use that particular submethod for its prediction.

Extensive information: Text file containing all information from the predictions. Each line starts with a four-letter tag, described below:
NAME   Name of sequence
ISTM   Either YES (=at least one TM region was predicted) or NO (=no TM regions were predicted)
Only given if ISTM = YES:
NTER   The predicted location of the N-terminus of the protein, either IN (cytoplasmic side) or OUT (extra-cytoplasmic side)
NRTM   The predicted number of TM regions in the protein
POSI   The positions of all predicted TM regions
RLTP   The reliability score for each position of the prediction (0-9)
RLTY   The reliability score for the whole prediction(0-100)
MTHD   The name of the prediction method for the following 'TOPO' lines
TOPO   The predicted topology of the protein, using the same format as in the Predicted topologies file

4. References

Rapid membrane protein topology prediction. Aron Hennerdal and Arne Elofsson (2011) Bioinformatics 27(9), 1322-3. [Pubmed]
TOPCONS: consensus prediction of membrane protein topology. Andreas Bernsel, Håkan Viklund, Aron Hennerdal and Arne Elofsson (2009) Nucleic Acids Research, Web Server Issue 37, W465-W468. [Pubmed]
Prediction of membrane-protein topology from first principles. Andreas Bernsel, Håkan Viklund, Jenny Falk, Erik Lindahl, Gunnar von Heijne and Arne Elofsson (2008) Proc. Natl. Acad. Sci. USA. 105, 7177-7181. [Pubmed]
Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Håkan Viklund and Arne Elofsson (2004) Protein Science, USA. 13, 1908-1917. [Pubmed]
The HMMTOP transmembrane topology prediction server. G E Tusnády and I Simon (2001) Bioinformatics 17(9), 849-850. [Pubmed]
A model recognition approach to the prediction of all-helical membrane protein structure and topology. D T Jones, W R Taylor and J M Thornton Biochemistry 33 (10) 3038-3049. [Pubmed]
A combined transmembrane topology and signal peptide prediction method. Lukas Käll, Anders Krogh, Erik L L Sonnhammer (2004) J. Mol. Biol. 338 (5), 1027-1036. [Pubmed]
Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. Gunnar von Heijne (1992) J. Mol. Biol. USA. 225(2), 487-494. [Pubmed]
TopPred II: an improved software for membrane protein structure predictions. Manuel G.CIaros, Gunnar von Heijne (1994) CABIOS, UK 10(6), 685-686. [Pubmed]

5. Contact

Arne Elofsson group

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

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

© 2010 Stockholm University, Stockholm Bioinformatics Centre, Center for Biomembrane Research