Skip to main content
Springer Nature Link
Log in

Comparison of Genomic DNA to cDNA Alignment Methods

  • Conference paper
Advances in Bioinformatics and Computational Biology (BSB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3594))

Included in the following conference series:

  • 866 Accesses

Abstract

Aligning cDNA sequences to genomic sequences is a very common way to study expressed sequences, find their genes, and study alternative splicing. Several computer programs address this problem, using heuristics to define exon regions. Usually, standard alignment algorithms are not used to align ESTs to genomic DNA, due to the existence of large regions of introns. This paper compares the EST-to-genomic alignments produced by sim4, est_genome, Spidey and standard sequence aligners using an appropriate score. Surprisingly, standard aligners performed quite well with sequences having few errors.

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

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. The Genome Sequencing Consortium. Initial sequencing and analysis of the human genome 409, 860–921 (2001)

    Google Scholar 

  2. Florea, L., Hartzell, G., Zhang, Z., Rubin, G., Miller, W.: A computer program for aligning cDNA sequence with genomic DNA sequence. Genome Research 8, 967–974 (1998)

    Google Scholar 

  3. Mott, R.: EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Computer Applications in the Biosciences 13, 477–478 (1997)

    Google Scholar 

  4. Myers, E.W., Miller, W.: Optimal alignment in linear space. Computer Applications in the Biosciences 4(1), 11–17 (1988)

    Google Scholar 

  5. National Center for Biotecnology Information, http://www.ncbi.nlm.nih.gov/

  6. Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America 85(8), 2444–2448 (1988), ftp://ftp.virginia.edu/pub/fasta/

    Article  Google Scholar 

  7. Rambaut, A., Grassly, N.C.: Seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13, 235–238 (1997)

    Google Scholar 

  8. Setubal, J.C., Meidanis, J.: Introduction to Computional Molecular Biology. PWS Publishing Company (1997)

    Google Scholar 

  9. Sorek, R., Safer, H.M.: A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Research 31(3), 1067–1074 (2003)

    Article  Google Scholar 

  10. Wheelan, S.J., Church, D.M., Ostell, J.M.: Spidey: A Tool for mRNA-to-Genomic Alignments. Genome Research 11, 1952–1957 (2001), Disponfvel em http://www.ncbi.nlm.nih.gov/spidey

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Instituto de Computação, Unicamp, Campinas, SP, Brasil

    Miguel Galves & Zanoni Dias

  2. Scylla Bioinformática, Campinas, SP, Brasil

    Miguel Galves & Zanoni Dias

Authors
  1. Miguel Galves
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zanoni Dias
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, Virginia Bioinformatics Institute and Virginia Polytechnic Institute and State University, Bioinformatics 1, Box 0477, 24060-0477, Blacksburg, VA, USA

    João Carlos Setubal

  2. Instituto de Quimica, Departamento de Bioquimica, Universidade de Sao Paulo, Av. Prof. Lineu Prestes 748, 05508-000, Sao Paulo, SP, Brazil

    Sergio Verjovski-Almeida

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Galves, M., Dias, Z. (2005). Comparison of Genomic DNA to cDNA Alignment Methods. In: Setubal, J.C., Verjovski-Almeida, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2005. Lecture Notes in Computer Science(), vol 3594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11532323_18

Download citation

  • DOI: https://doi.org/10.1007/11532323_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28008-8

  • Online ISBN: 978-3-540-31861-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics