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Bioinformatics in protein analysis

  • Chapter
Proteomics in Functional Genomics

Part of the book series: EXS ((EXS,volume 88))

Summary

The chapter gives an overview of bioinformatic techniques of importance in protein analysis. These include database searches, sequence comparisons and structural predictions. Links to useful World Wide Web (WWW) pages are given in relation to each topic.

Databases with biological information are reviewed with emphasis on databases for nucleotide sequences (EMBL, GenBank, DDBJ), genomes, amino acid sequences (Swissprot, PIR, TrEMBL, GenePept), and three-dimensional structures (PDB). Integrated user interfaces for databases (SRS and Entrez) are described. An introduction to databases of sequence patterns and protein families is also given (Prosite, Pfam, Blocks).

Furthermore, the chapter describes the widespread methods for sequence comparisons, FASTA and BLAST, and the corresponding WWW services. The techniques involving multiple sequence alignments are also reviewed: alignment creation with the Clustal programs, phylogenetic tree calculation with the Clustal or Phylip packages and tree display using Drawtree, njplot or phylo_win.

Finally, the chapter also treats the issue of structural prediction. Different methods for secondary structure predictions are described (Chou-Fasman, Garnier-Osguthorpe-Robson, Predator, PHD). Techniques for predicting membrane proteins, antigenic sites and postranslational modifications are also reviewed.

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Author information

Authors and Affiliations

  1. Stockholm Bioinformatic Centre and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177, Sweden

    Bengt Persson

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  1. Bengt Persson
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Editor information

Editors and Affiliations

  1. Laboratoire de Chimie des Substances Naturelles URA C.N.R.S. No. 401, Muséum National d’Histoire Naturelle, 63, rue Buffon, F-75005, Paris, France

    P. Jollès

  2. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden

    H. Jörnvall

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© 2000 Springer Basel AG

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Persson, B. (2000). Bioinformatics in protein analysis. In: Jollès, P., Jörnvall, H. (eds) Proteomics in Functional Genomics. EXS, vol 88. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8458-7_14

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  • DOI: https://doi.org/10.1007/978-3-0348-8458-7_14

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-0348-9576-7

  • Online ISBN: 978-3-0348-8458-7

  • eBook Packages: Springer Book Archive

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