Abstract
The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
Keywords
References
CATH: Protein Structure Classification Database at UCL, http://www.cathdb.info (Online; last accessed December 10, 2012)
EBI Web Services, http://www.ebi.ac.uk/Tools/webservices/ (Online; last accessed December 10, 2012)
Pfam: Home page, http://pfam.sanger.ac.uk/ (Online; last accessed December 06, 2012)
RCSB Protein Data Bank - RCSB PDB, http://www.rcsb.org/pdb/home/home.do (Online; last accessed December 06, 2012)
SCOP: Structural Classification of Proteins, http://scop.mrc-lmb.cam.ac.uk/scop/ (Online; last accessed December 10, 2012)
Blaese, L.: Data Mining for Unidentified Protein Sequences. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 73–87. Springer, Heidelberg (2014)
Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: Automating Metabolic Flux Analysis. Metabolites 2(4), 872–890 (2012)
Garnier, J., Gibrat, J.-F., Robson, B.: GOR method for predicting protein secondary structure from amino acid sequence. In: Doolittle, R.F. (ed.) Computer Methods for Macromolecular Sequence Analysis. Methods in Enzymology, vol. 266, pp. 540–553. Academic Press (1996)
Lamprecht, A.-L. (ed.): User-Level Workflow Design. LNCS, vol. 8311. Springer, Heidelberg (2013)
Lamprecht, A.-L., Margaria, T.: Scientific Workflows and XMDD. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 1–13. Springer, Heidelberg (2014)
Lamprecht, A.-L., Margaria, T., Steffen, B.: Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI. In: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 445–456. Springer, Heidelberg (2008)
Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: A framework for semantics-based service composition. BMC Bioinformatics 10(suppl. 10), S8 (2009)
Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics 9 (suppl. 4), S13 (2008)
Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. Journal of Biomedical Semantics 2(suppl. 1), S5 (2011)
Lamprecht, A.-L., Wickert, A.: The Course’s SIB Libraries. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 30–44. Springer, Heidelberg (2014)
Lis, M.: Constructing a Phylogenetic Tree. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 101–109. Springer, Heidelberg (2014)
Margaria, T., Steffen, B.: Agile IT: Thinking in User-Centric Models. In: Margaria, T., Steffen, B. (eds.) ISoLA 2008. CCIS, vol. 17, pp. 490–502. Springer, Heidelberg (2009)
Margaria, T., Steffen, B.: Business Process Modelling in the jABC: The One-Thing-Approach. In: Cardoso, J., van der Aalst, W. (eds.) Handbook of Research on Business Process Modeling. IGI Global (2009)
Margaria, T., Steffen, B.: Continuous Model-Driven Engineering. IEEE Computer 42(10), 106–109 (2009)
Margaria, T., Steffen, B.: Simplicity as a Driver for Agile Innovation. Computer 43(6), 90–92 (2010)
Margaria, T., Steffen, B.: Service-Orientation: Conquering Complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, London (2012)
Margaria, T., Steffen, B., Reitenspieß, M.: Service-Oriented Design: The Roots. In: Benatallah, B., Casati, F., Traverso, P. (eds.) ICSOC 2005. LNCS, vol. 3826, pp. 450–464. Springer, Heidelberg (2005)
Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose Programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) Fundamental Approaches to Software Engineering. LNCS, vol. 7212, pp. 94–98. Springer, Heidelberg (2012)
Schütt, C.: Identification of Differentially Expressed Genes. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 127–139. Springer, Heidelberg (2014)
Schulze, G.: Workflow for Rapid Metagenome Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 88–100. Springer, Heidelberg (2014)
Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-Driven Development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, pp. 92–108. Springer, Heidelberg (2007)
Vierheller, J.: Exploratory Data Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 110–126. Springer, Heidelberg (2014)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Reso, J. (2014). Protein Classification Workflow. In: Lamprecht, AL., Margaria, T. (eds) Process Design for Natural Scientists. Communications in Computer and Information Science, vol 500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45006-2_5
Download citation
DOI: https://doi.org/10.1007/978-3-662-45006-2_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-45005-5
Online ISBN: 978-3-662-45006-2
eBook Packages: Computer ScienceComputer Science (R0)