Chapter 1. The Basics of Protein Sequence Analysis

  1. Janusz M. Bujnicki1,2
  1. Katarzyna H. Kaminska1,2,
  2. Kaja Milanowska2 and
  3. Janusz M. Bujnicki1,2

Published Online: 18 DEC 2008

DOI: 10.1002/9780470741894.ch1

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions

How to Cite

Kaminska, K. H., Milanowska, K. and Bujnicki, J. M. (2008) The Basics of Protein Sequence Analysis, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch1

Editor Information

  1. 1

    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

  2. 2

    Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland

Author Information

  1. 1

    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

  2. 2

    Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland

Publication History

  1. Published Online: 18 DEC 2008
  2. Published Print: 19 DEC 2008

ISBN Information

Print ISBN: 9780470517673

Online ISBN: 9780470741894

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Keywords:

  • protein sequence analysis basics;
  • protein-encoding genes and duplications;
  • domains - protein sequence primary functional units;
  • gene fragment encoding domains;
  • protein families databases - domains and motifs;
  • database searches and pairwise alignments;
  • sequence alignment - global Needleman-Wunsch and local Smith-Waterman;
  • multiple sequence alignment;
  • domain prediction

Summary

This chapter contains sections titled:

  • Introduction

  • Domains: Primary Functional Units in Protein Sequence

  • Sequence Motifs

  • Databases of Protein Families, Domains, and Motifs

  • Database Searches and Pairwise Alignments

  • Sequence Clustering

  • Multiple Sequence Alignment

  • Relationship of Multiple Sequence Alignments to Phylogenetic Analysis

  • Prediction of Domains

  • Summary

  • Acknowledgements

  • References