Abstract
After sequence data is obtained from the laboratory there is still a lot of time consuming manual post-processing necessary until the data is ready for submission to one of the sequence databases. One of the most time consuming activities called editing is to find and correct faulty base calls in the sequences by looking at the original electrophoresis trace data. Our efforts in this project aim towards developing appropriate methods and tools to reduce the time the editor (our expert) has to spend for this post-processing. Therefore we intend to automatically perform as much of this sequence editing as possible. A first prototype with limited competence was implemented and evaluated. This paper discusses the issues involved in this evaluation. We elucidate why it can be reasonable to evaluate a system at a very early point in time, explain how this evaluation was conducted and present the results obtained.
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References
Bonfield, J.K., Staden, R.: The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Research 23(8), 1406–1410 (1995)
Breuker, J., Van der Velde, W. (eds.): CommonKADS Library for Expertise Modelling. IOS Press Amsterdam, Amsterdam (1994)
Casey, D.: Primer on molecular genetics. US Department of Energy (1992) http://www.ornl.gov/hgmis/publicat/primer/intro.html
Dear, S., Durbin, R., Hillier, L., Gabor, M., Thierry-Mieg, J., Mott, R.: Sequence assembly with CAFTOOLS. Genome Research 8, 260–267 (1998)
Ewing, B., Green, P.: Base-calling of automated sequencer traces using PHRED. II. error probabilities. Genome Research 8(3), 167–194 (1998)
Lawrence, C.B., Solovyev, V.V.: Assignment of position-specific error pro-bability to primary DNA sequence data. Nucleic Acids Research 22(7), 1272–1280 (1994)
Lipshutz, R.J., Taverner, F., Hennessy, K., Hartzell, G., Davis, R.: DNA sequence confidence estimation. Genomics 19(3), 417–424 (1994)
Mott, R.: Trace alignment and some of its applications. Bioinformatics 14(1), 92–97 (1998)
Setubal, J., Meidanis, J.: Introduction to computational molecualar biology. PWS Publishing Company (1997)
Wetter, T., Pfisterer, T.: Modeling for scalability - ascending into automatic genome sequencing. In: Eleventh Workshop on Knowledge Acquisition, Modeling and Management (KAW 1998), Banff (Canada), April 14-18 (1998)
Wielinga, B.J., Schreiber, B.J., Breuker, J.A.: KADS: a modelling approach to knowledge engineering. Knowledge Acquisition 4(1), 5–54 (1992)
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© 1999 Springer-Verlag Berlin Heidelberg
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Pfisterer, T., Wetter, T. (1999). Computer Assisted Editing of Genomic Sequences – Why and how We Evaluated a Prototype. In: Puppe, F. (eds) XPS-99: Knowledge-Based Systems. Survey and Future Directions. XPS 1999. Lecture Notes in Computer Science(), vol 1570. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10703016_16
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DOI: https://doi.org/10.1007/10703016_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-65658-6
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