Chapter 13. Database Searching for de novosequences

  1. Ingvar Eidhammer1,
  2. Kristian Flikka1,
  3. Lennart Martens2 and
  4. Svein-Ole Mikalsen3

Published Online: 10 DEC 2007

DOI: 10.1002/9780470724309.ch13

Computational Methods for Mass Spectrometry Proteomics

Computational Methods for Mass Spectrometry Proteomics

How to Cite

Eidhammer, I., Flikka, K., Martens, L. and Mikalsen, S.-O. (2007) Database Searching for de novosequences, in Computational Methods for Mass Spectrometry Proteomics, John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470724309.ch13

Author Information

  1. 1

    University of Bergen, Norway

  2. 2

    European Bioinformatics Institute, Hinxton, Cambridge, UK

  3. 3

    The Norwegian Radium Hospital, Oslo, Norway

Publication History

  1. Published Online: 10 DEC 2007
  2. Published Print: 30 NOV 2007

ISBN Information

Print ISBN: 9780470512975

Online ISBN: 9780470724309

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Keywords:

  • amino acid residue masses;
  • database sequence and individual query matches;
  • peptide sequence and extract sequence tags;
  • spectrum graph and suffix tree;
  • non-deterministic finite automaton (NDFA)

Summary

This chapter contains sections titled:

  • Using general sequence search programs

  • Specialized search programs

  • Peptide sequence tags

  • Comparison by threading

  • Exercises

  • Bibliographic notes