Publication
| 1. |
Magner, J.A. 1982. Information in the signal peptide? J Theor Biol 99: 831-833. |
| 2. |
Boerwinkle, E., S.H. Chen, S. Visvikis, C.L. Hanis, G. Siest, and L. Chan. 1991. Signal peptide-length variation in human apolipoprotein B gene. Molecular characteristics and association with plasma glucose levels. Diabetes 40: 1539-1544. |
| 3. | Jain, R.G., S.L. Rusch, and D.A. Kendall. 1994. Signal peptide cleavage regions. Functional limits on length and topological implications. J Biol Chem 269: 16305-16310. |
| 4. | von Heijne, G. 1990. The signal peptide. J Membr Biol 115: 195-201. |
| 5. | von Heijne, G. 1998. Life and death of a signal peptide. Nature 396: 111, 113. |
| 6. | Morrison, G.M., C.A. Semple, F.M. Kilanowski, R.E. Hill, and J.R. Dorin. 2003. Signal sequence conservation and mature peptide divergence within subgroups of the murine beta-defensin gene family. Mol Biol Evol 20: 460-470. |
| 7. | Chen, M. and V. Nagarajan. 1993. The roles of signal peptide and mature protein in RNase (barnase) export from Bacillus subtilis. Mol Gen Genet 239: 409-415. |
| 8. | Nothwehr, S.F. and J.I. Gordon. 1989. Eukaryotic signal peptide structure/function relationships. Identification of conformational features which influence the site and efficiency of co-translational proteolytic processing by site-directed mutagenesis of human pre(delta pro)apolipoprotein A-II. J Biol Chem 264: 3979-3987. |
| 9. | McGeoch, D.J. 1985. On the predictive recognition of signal peptide sequences. Virus Res 3: 271-286. |
| 10. | Roy, P., C. Chatellard, G. Lemay, P. Crine, and G. Boileau. 1993. Transformation of the signal peptide/membrane anchor domain of a type II transmembrane protein into a cleavable signal peptide. J Biol Chem 268: 2699-2704. |
| 11. | von Heijne, G. and L. Abrahmsen. 1989. Species-specific variation in signal peptide design. Implications for protein secretion in foreign hosts. FEBS Lett 244: 439-446. |
| 12. | Nielsen H., Engelbrecht J., Brunak S., Heijne G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6. |
| 13. | Juncker A.S., Willenbrock H., Heijne G., Nielsen H., Brunak S. and Krogh A., 2003. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 12(8):1652-62. |
| 14. | Kall L., Krogh A. and Sonhammer E., 2004. A combined transmembrane topology and signal peptide prediction method. Journal of Mol.Bio., 338(5):1027-1036. |
| 15. | Reczko M., Staub E., Fiziev P., 2002. Finding signal peptides in human protein sequences using recurrent neural networks. Proceedings of 2nd Int. Workshop WABI, Sep 16-21. |
| 16. | Ladunga, I., F. Czako, I. Csabai, and T. Geszti. 1991. Improving signal peptide prediction accuracy by simulated neural network. Comput Appl Biosci 7: 485-487. |
| 17. | Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O’Donovan C, Phan I., Pilbout S., Schneider M.,The Swiss-Prot protein sequence knowledgebase and its supplement TrEMBL, Nucleic Acids Res. 31:365-370, 2003. |
| 18. | Bendtsen, J.D., Henrik Nielsen, Gunnar von Heijne and Søren Brunak. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340:783-795. |
| 19. | Klein, B.K., J.O. Polazzi, C.S. Devine, S.H. Rangwala, and P.O. Olins. 1992. Effects of signal peptide changes on the secretion of bovine somatotropin (bST) from Escherichia coli. Protein Eng 5: 511-517. |
| 20. | Rusch, S.L., H. Chen, J.W. Izard, and D.A. Kendall. 1994. Signal peptide hydrophobicity is finely tailored for function. J Cell Biochem 55: 209-217. |
| 21. | San Miguel, M., R. Marrington, P.M. Rodger, A. Rodger, and C. Robinson. 2003. An Escherichia coli twin-arginine signal peptide switches between helical and unstructured conformations depending on the hydrophobicity of the environment. Eur J Biochem 270: 3345-3352. |
| 22. | Nilsson, I. and G. von Heijne. 1992. A signal peptide with a proline next to the cleavage site inhibits leader peptidase when present in a sec-independent protein. FEBS Lett 299: 243-246. |
| 23. | Kyte J., Doolittle R.F. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol May 5;157(1):105-132. |
| 24. | Sweet R.M., Eisenberg D. 1983. Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol Dec 25;171(4):479-488. |
| 25. | Eisenberg D., Weiss R.M., Terwilliger T.C. 1982. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature Sep 23;299(5881):371-4. |
| 26. | Kulikova T., Aldebert P., Althorpe N., Baker W., Bates K., Browne P.,
Van Den Broek A., Cochrane G., Duggan K., Eberhardt R., Faruque N.,
Garcia-Pastor M., Harte N., Kanz C., Leinonen R., Lin Q., Lombard V.,
Lopez R., Mancuso R., McHale M., Nardon F., Silventoinen V., Stoehr P.,
Stoesser G., Tuli M.A., Tzouvara K., Vaughan R., Wu D., Zhu W.,
Apweiler R. 2004.
The EMBL Nucleotide Sequence Database.
Nucleic Acids Res.32: D27-D30.
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| 27. | Nielsen H, Engelbrecht J, von Heijne G, Brunak S. 1996. Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site. Proteins. Feb;24(2):165-77.
|
| 28. | Rice P., Longden I. and Bleasby A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16,(6) 276-277.
|
| 29. | Kanz C., Aldebert P., Althorpe N., Bakero W., Baldwin A., Bates K., Browne P., van den Broek A., Castro M., Cochrane G., Duggan K., Eberhardt R., Faruque N., Gamble J., Garcia Diez F., Harte N., Kulikova T., Lin Q., Lombard V., Lopez R., Mancuso R., McHale M., Nardone F., Silventoinen V., Sobhany S., Stoehr P., Tuli M.A., Tzouvara K., Vaughan R., Wu D., Zhu W.M. and Apweiler R. 2005. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33: D29-D33 |
| 30. | Brown, NP., Leroy C., Sander C. 1998. MView: A Web compatible database search or multiple alignment viewer. Bioinformatics 14: 380-381.
|
| 31. | Zhang Z., Henzel W.J. 2004. Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Sci. 13:2819-2824.
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Websites (Databases & Prediction Servers)
Miscellaneous
The text below were extracted from Swiss-Prot Manual for quick reference. Some of the text were omitted for brevity and relevance. To read the full manual, click here :
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| 2.4. Non-experimental qualifiers |
3 types of non-experimental qualifiers in comment (CC) lines and feature table (FT lines) indicate that the information given is not based on experimentally proven findings:
- Potential
- Probable
- By similarity
The term 'Potential' indicates that there is some logical or conclusive evidence that the given annotation could apply. This non-experimental qualifier is often used to present the results from protein sequence analysis tools, which are only annotated, if the result makes sense in the context of a given protein. A typical example is the annotation of N-glycosylation sites in the entries of non-cytoplasmic domains or proteins.
The term 'Probable' counts stronger than the qualifier 'Potential' and there must be at least some experimental evidence, which indicates, that the given information is expected to be found in the natural environment of a protein.
'By similarity' is added to facts that were proven for a protein or part of it, and which is then transferred to the proteins of related organisms. This non-experimental qualifier is also used to transfer the information on known biological important sites within conserved domains to proteins that contain one or more copies of such a domain, e.g. active sites within an enzymatic domain or disulfide bonds, which stabilize the structure of extracellular modules.
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| »» To read the full Swis-Prot manual, click here |
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| 3.7. The OG line |
The OG (OrGanelle) line indicates if the gene coding for a protein originates from the mitochondria, the chloroplast, the cyanelle, the nucleomorph or a plasmid.
The format of the OG line is:
OG Chloroplast.
OG Cyanelle.
OG Mitochondrion.
OG Nucleomorph.
OG Plasmid name.
Where 'name' is the name of the plasmid.
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| »» To read the full Swis-Prot manual, click here |
|
| 3.15. The FT line |
The FT (Feature Table) lines provide a precise but simple means for the annotation of the sequence data. The table describes regions or sites of interest in the sequence. In general the feature table lists posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. Sequence conflicts between references are also included in the feature table.
Example of a FT line in Swiss-Prot entry :
FT NON_TER 1 1
FT SIGNAL <1 10 By similarity.
The first item on each FT line is the key name, which is a fixed abbreviation (of up to 8 characters) with a defined meaning. A list of the currently defined key names can be found in Appendix A of this document.
Following the key name are the 'FROM' and 'TO' endpoint specifications. These fields designate (inclusively) the endpoints of the feature named in the key field. In general, these fields simply contain residue numbers which indicate positions in the sequence as listed. Note that these positions are always specified assuming a numbering of the listed sequence from 1 to n; this numbering is not necessarily the same as that used in the original reference(s). The following should be noted:
If the 'FROM' and 'TO' specifications are identical, the feature involves one single amino acid;
When a feature is known to extend beyond the position that is given in the feature table, the endpoint specification will be preceded by '<' for features which continue to the left end (N-terminal direction) or by '>' for features which continue to the right end (C- terminal direction);
Unknown endpoints are denoted by '?'. Uncertain endpoints are denoted by a '?' before the position, e.g. '?42'.
The remaining portion of the FT line is a description that contains additional information about the feature. For example, for a posttranslationally modified residue (key MOD_RES) the chemical nature of the modified residue is given, while for a sequence variation (key VARIANT) the nature of the variation is indicated. This portion of the line is generally in free form, and may be continued on additional lines when necessary.
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| »» To read the full Swis-Prot manual, click here |
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