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Genomic database applications in DISCO

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Constraint Databases and Applications (CDB 1997)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1191))

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Abstract

A genome map is an ordering of a set of clones according to their believed position on a DNA string. Simple heuristics for genome map assembly based on single restriction enzyme with complete digestion data can lead to inaccuracies and ambiguities. This paper presents a method that adds additional constraint checking to the assembly process. An automaton is presented that for any genome map produces a refined genome map where both the clones and the restriction fragments in each clone are ordered satisfying natural constraints called step constraints. Any genome map that cannot be refined is highly likely to be inaccurate and can be eliminated as a possibility.

This work was supported in part by NSF grants IRI-9625055 and IRI-9632871.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, University of Nebraska, 68588, Lincoln, NE, USA

    Peter Z. Revesz

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  1. Peter Z. Revesz
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Editor information

Volker Gaede Alexander Brodsky Oliver Günther Divesh Srivastava Victor Vianu Mark Wallace

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© 1996 Springer-Verlag Berlin Heidelberg

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Revesz, P.Z. (1996). Genomic database applications in DISCO. In: Gaede, V., Brodsky, A., Günther, O., Srivastava, D., Vianu, V., Wallace, M. (eds) Constraint Databases and Applications. CDB 1997. Lecture Notes in Computer Science, vol 1191. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-62501-1_35

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  • DOI: https://doi.org/10.1007/3-540-62501-1_35

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-62501-8

  • Online ISBN: 978-3-540-68049-9

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