Information

The data in this web tool is supported by our publication: Weill, Cohen et al, BioEssays 2019
How to cite: Weill U, Cohen N, Fadel A, Ben-Dor S & Schuldiner M. Protein topology prediction algorithms systematically investigated in the yeast Saccharomyces cerevisiae. BioEssays 2019

All Gene Information was taken from the Saccharomyces Genome Database (SGD) (Cherry et al., 2012)

We did not make any of the prediction algorithms rather simply compiled their output in one place. We take not credit nor responsibility for their performance. Specifically, we used the following prediction algorithms for:

TOPOLOGY

  • TMHMM (Krogh et al., 2001),(Reynolds et al., 2008)
  • Phobius (Käll et al., 2004)
  • Topcons (Bernsel et al., 2009)
  • Octopus (Viklund and Elofsson, 2008)
  • Polyphobius (Kall et al., 2005)
  • Scampi (Bernsel et al., 2008)
  • Spoctopus (Viklund et al., 2008)
  • HMMTOP (Tusnády and Simon, 2001)
  • MEMSAT-SVM (Nugent and Jones, 2009)

SIGNAL PEPTIDES

  • SignalP 4.1 (Petersen et al., 2011)

MITOCHONDRIAL TARGETING SEQEUNCES

  • Mitofates (Fukasawa et al., 2015)
  • TargetP version 1.1 (Emanuelsson et al., 2007)
     

Finally, we compiled experimental data from three papers:

  • Presence of an experimentally verified MTS: (Venne et al., 2013; Vögtle et al., 2009)
  • Localization with an N’ tag or orientation of N’ for TMD proteins: (Weill et al., 2018)
  • Localization with a C’ tag : (Huh et al., 2003)

REFERENCES

  • Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G., and Elofsson, A. (2008). Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. U. S. A. 105, 7177–7181.
  • Bernsel, A., Viklund, H., Hennerdal, A., and Elofsson, A. (2009). TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 37, W465-8.
  • Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Karra, K., Krieger, C.J., Miyasato, S.R., Nash, R.S., Park, J., Skrzypek, M.S., Simison, M., Weng, S., Wong, E.D. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res.40, D700-5
  • Emanuelsson, O., Brunak, S., von Heijne, G., and Nielsen, H. (2007). Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2, 953–971.
  • Fukasawa, Y., Tsuji, J., Fu, S.-C., Tomii, K., Horton, P., and Imai, K. (2015). MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites. Mol. Cell. Proteomics 14, 1113–1126.
  • Kall, L., Krogh, A., and Sonnhammer, E.L.L. (2005). An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21, i251–i257.
  • Käll, L., Krogh, A., and Sonnhammer, E.L.L. (2004). A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338, 1027–1036.
  • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.. (2001). Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen. J. Mol. Biol. 305, 567–580.
  • Petersen, T.N., Brunak, S., von Heijne, G., and Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786.
  • Reynolds, S.M., Käll, L., Riffle, M.E., Bilmes, J.A., and Noble, W.S. (2008). Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol. 4, e1000213.
  • Venne, A.S., Vögtle, F.-N., Meisinger, C., Sickmann, A., and Zahedi, R.P. (2013). Novel Highly Sensitive, Specific, and Straightforward Strategy for Comprehensive N-Terminal Proteomics Reveals Unknown Substrates of the Mitochondrial Peptidase Icp55. J. Proteome Res. 12, 3823–3830.
  • Viklund, H., and Elofsson, A. (2008). OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 24, 1662–1668.
  • Viklund, H., Bernsel, A., Skwark, M., and Elofsson, A. (2008). SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24, 2928–2929.
  • Vögtle, F.-N., Wortelkamp, S., Zahedi, R.P., Becker, D., Leidhold, C., Gevaert, K., Kellermann, J., Voos, W., Sickmann, A., Pfanner, N., et al. (2009). Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139, 428–439.
  • Weill, U., Yofe, I., Sass, E., Stynen, B., Davidi, D., Natarajan, J., Ben-Menachem, R., Avihou, Z., Goldman, O., Harpaz, N., et al. (2018). Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat. Methods 15, 617–622.