Skip to main content

Biological Sequence Assembly and Alignment

  • Chapter
Bioinformatics Technologies

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Bonfield, J.K., Smith, K.F., and Staden, R. (1995) A New DNA Sequence Assembly Program. Nucleic Acids Research 23: 4992–4999.

    Google Scholar 

  • Carol, A. Dahl, Robert, L. and Strausberg (1996.1) Human Genome Project: Revolutionizing Biology Through Leveraging Technology. Proceedings of SPIE-The International Society for Optical Engineering, pp 190–201.

    Google Scholar 

  • Green, P. (1999) Documentation for Phrap and Cross-Match (Version 0. 990319). http://www.genome.washington.edu/UWGC/analysistools/Phrap.cfm

    Google Scholar 

  • Huang, X., Madan, A. (1999) CAP3: A DNA Sequence Assembly Program. Genome Research 9: 868–877.

    Article  Google Scholar 

  • Julie, D.T., Desmond, G.H., Toby, J.G. and Clustal, W. (1994) Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucl. Acid Res. 22: 4673–4680.

    Google Scholar 

  • Kececioglu, J. and Myers, E. (1995) Combinatorial Algorithms for DNA Sequence Assembly. Algorithmica 13: 7–51.

    MathSciNet  Google Scholar 

  • Liming, C., David, J. and Evgueni, L. (2000) Evolutionary Computation Techniques for Multiple Sequence Alignment. Proceedings of the IEEE Conference on Evolutionary Computation. San Diego 7: 829–835.

    Google Scholar 

  • Myers, E.M. (2002) Toward Simplifying and Accurately Formulating Fragment Assembly. Journal of Computational Biology 2(2): 275–290.

    Google Scholar 

  • Pavel, A., Pevzner and Haixu, T. and Waterman, S. (2001) An Eulerian Path Approach to DNA Fragment Assembly. Proceedings of National Academy of Sciences of the United States of America 98(17): 9748–9753.

    Google Scholar 

  • Rajkumar, B. (1999) High Performance Cluster Computing. Vol. 1, Architecture and Systems, Vol. 2, Programming and Applications, Prentice Hall, Upper Saddle River, New Jersey, USA.

    Google Scholar 

  • Shamir, R. and Tsur, D. (2002.5) Large Scale Sequencing by Hybridization. Proceedings of the Annual International Conference on Computational Molecular Biology, pp 269–277.

    Google Scholar 

  • Sutton, G., White, O., Adams, M. and Kerlavage, A. (1995) TIGR assembler: A New Tool for Assembling Large Shotgun Sequencing Projects, Genome Science and Technology 1: 9–19.

    Google Scholar 

  • Temple, F.S. and Michael, S.W. (1981) Identification of Common Molecular Subsequences. J. Mol. Bio. 147: 195–197.

    Google Scholar 

  • Terry A Braun, Todd E Scheetz, Gregg Webster, Abe Clark, Edwin M Stone, Val C Sheffield, Thomas L Casavant (2003) Identifying Candidate Disease Genes with High-Performance Computing. The Journal of Supercomputing 26(1): 7–24

    Article  Google Scholar 

  • The Institute for Genomic Research (2003) Benchmark Data for Genome Assembly. http://www.tigr.org/tdb/benchmark/

    Google Scholar 

  • Weber, J. and Myers, G. (1997) Whole Genome Shotgun Sequencing. Genome Research 7: 401–409.

    Google Scholar 

  • Wei, S and Wanlei, Z. (2003.12) Large-Scale Biological Sequence Assembly and Alignment by Using Computing Grid, Lecture Notes in Computer Science, Springer-Verlag.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Hiedelberg

About this chapter

Cite this chapter

Shi, W., Zhou, W., Chen, YP.P. (2005). Biological Sequence Assembly and Alignment. In: Chen, YP.P. (eds) Bioinformatics Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26888-X_8

Download citation

  • DOI: https://doi.org/10.1007/3-540-26888-X_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20873-0

  • Online ISBN: 978-3-540-26888-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics