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Automatic Assembly and Editing of Genomic Data

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References

  1. Bonfield, J.K., Smith, K.F., and Staden, R. (1995). A new DNA sequence assembly program. Nucleic Acids Research, 23(24):4992–9.

    PubMed  CAS  Google Scholar 

  2. Bonfield, J.K.and Staden, R. (1995). The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Research, 23(8):1406–10.

    PubMed  CAS  Google Scholar 

  3. Breuker, J. and der Velde, W.V., editors (1994). CommonKADS Library for Expertise Modelling. IOS Press Amsterdam.

    Google Scholar 

  4. Dear, S., Durbin, R., Hillier, L., Gabor, M., Thierry-Mieg, J., and Mott, R. (1998). Sequence assembly with CAFTOOLS. Genome Research, 8:260–7.

    PubMed  CAS  Google Scholar 

  5. Dear, S. and Staden, R.(1992). A standard file format for data from DNA sequencing instruments. DNA Sequence, 3:107–10.

    PubMed  CAS  Google Scholar 

  6. Ewing, B. and Green, P. (1998). Base-calling of automated sequencer traces using PHRED. II. error probabilities. Genome Research, 8(3):186–94.

    PubMed  CAS  Google Scholar 

  7. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. (1998). Base-calling of automated sequencer traces using phred. I. accuracy assessment. Genome Research, 8(3):175–85.

    PubMed  CAS  Google Scholar 

  8. Gordon, D., Abajian, C., and Green, P. (1998). consed: A graphical tool for sequence finishing. Genome Research, 8(3):195–202.

    PubMed  CAS  Google Scholar 

  9. Lario, A, Gonzalez, A, and Dorado, G. (1997). Automated laser-induced fluorescence DNA sequencing: Equalizing signal-to-noise ratios significantly enhances overall performance. Analytical Biochemistry, 247:30–3.

    Article  PubMed  CAS  Google Scholar 

  10. Lawrence, C.B. and Solovyev, V.V. (1994). Assignment of position-specific error probability to primary DNA sequence data. Nucleic Acids Research, 22(7):1272–80.

    PubMed  CAS  Google Scholar 

  11. Lipshutz, R.J., Taverner, F., Hennessy, K., Hartzell, G., and Davis, R. (1994). DNA sequence confidence estimation. Genomics, 19(3):417–24.

    Article  PubMed  CAS  Google Scholar 

  12. Mott, R. (1998). Trace alignment and some of its applications. Bioinformatics, 14(1):92–7.

    Article  PubMed  CAS  Google Scholar 

  13. Pfisterer, T. and Wetter, T. (1999). Computer assisted editing of genomic sequences—why and how we evaluated a prototype. In: Puppe, F. (editor): XPS-99: Knowledge-Based Systems—Survey and Future Directions, 201-209, Springer.

    Google Scholar 

  14. Sedgewick, R. (1994). Algorithmen in C++. Addison-Wesley [Deutschland] GmbH.

    Google Scholar 

  15. Wang, L. and Jiang, T. (1994). On the complexity of multiple sequence alignment. Journal of Computational Biology, 1(4):337–48.

    Article  PubMed  CAS  Google Scholar 

  16. Wetter, T. and Pfisterer, T. (April 14–18, 1998). Modeling for scalability—ascending into automatic genome sequencing. In Eleventh Workshop on Knowledge Acquisition, Modeling and Management (KAW’98), Banff (Canada).

    Google Scholar 

  17. Wielinga, B.J., Schreiber, B.J., and Breuker, J.A. (1992). KADS: amodelling approach to knowledge engineering. Knowledge Acquisition, 4(1):5–54.

    Article  Google Scholar 

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© 2002 Kluwer Academic Publishers

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Chevreux, B., Pfisterer, T., Suhai, S. (2002). Automatic Assembly and Editing of Genomic Data. In: Suhai, S. (eds) Genomics and Proteomics. Springer, Boston, MA. https://doi.org/10.1007/0-306-46823-9_5

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  • DOI: https://doi.org/10.1007/0-306-46823-9_5

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-306-46312-9

  • Online ISBN: 978-0-306-46823-0

  • eBook Packages: Springer Book Archive

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