Skip to main content

Protein Alignments

  • Chapter
  • 4047 Accesses

Part of the book series: Modeling and Optimization in Science and Technologies ((MOST,volume 6))

Abstract

Protein sequence data has begun playing a significant role in biology and biochemistry. In the past, protein sequence determination was usually one of the last steps in the characterization of a protein. Given the advancements of the Human Genome Project, one can first sequence all the genes and use sequence analysis to infer function using sequence alignment methods.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ma, J., Wang, S.: Algorithms, applications, and challenges of protein structure alignment. Adv. Protein Chem. Struct. Biol. 94, 121–175 (2014)

    Article  Google Scholar 

  2. Stamm, M., Staritzbichler, R., Khafizov, K., Forrest, L.R.: Alignme–a membrane protein sequence alignment web server. Nucleic Acids Res (April 2014)

    Google Scholar 

  3. Ritchie, D.W., Ghoorah, A.W., Mavridis, L., Venkatraman, V.: Fast protein structure alignment using gaussian overlap scoring of backbone peptide fragment similarity. Bioinformatics 28(24), 3274–3281 (2012)

    Article  Google Scholar 

  4. Léonard, S., Joseph, A.P., Srinivasan, N., Gelly, J.-C., de Brevern, A.G.: mulpba: an efficient multiple protein structure alignment method based on a structural alphabet. J. Biomol. Struct. Dyn. 32(4), 661–668 (2014)

    Article  Google Scholar 

  5. Arriagada, M., Poleksic, A.: On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem. Biomed. Res. Int. 459248 (2013)

    Google Scholar 

  6. Dayhoff, M.O., Orcutt, B.C.: Methods for identifying proteins by using partial sequences. Proc. Natl. Acad. Sci. U S A 76(5), 2170–2174 (1979), Journal Article Research Support, U.S. Gov’t, P.H.S. United states

    Google Scholar 

  7. George, D.G., Barker, W.C., Hunt, L.T.: Mutation data matrix and its uses. Methods Enzymol 183, 333–351 (1990), Gm37273/gm/nigms Journal Article Research Support, U.S. Gov’t, P.H.S. United states

    Google Scholar 

  8. Altschul, S.F.: Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219(3), 555–565 (1991), Comparative Study Journal Article England

    Google Scholar 

  9. Karlin, S., Altschul, S.F.: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U S A 87(6), 2264–2268 (1990), Gm10452-26/gm/nigms Gm39907-02/gm/nigms Journal Article Research Support, U.S. Gov’t, Non-P.H.S. Research Support, U.S. Gov’t, P.H.S. United states

    Google Scholar 

  10. Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U S A 89(22), 10915–10919 (1992), Comparative Study Journal Article Research Support, U.S. Gov’t, P.H.S. United states

    Google Scholar 

  11. Henikoff, S., Henikoff, J.G., Alford, W.J., Pietrokovski, S.: Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene. 163(2), GC17–GC26 (1995), Gm29009/gm/nigms Comparative Study Journal Article Research Support, U.S. Gov’t, P.H.S. Netherlands

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gautam B. Singh .

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Singh, G.B. (2015). Protein Alignments. In: Fundamentals of Bioinformatics and Computational Biology. Modeling and Optimization in Science and Technologies, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-319-11403-3_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-11403-3_6

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11402-6

  • Online ISBN: 978-3-319-11403-3

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics