Directed Gap Closure in Large-Scale Sequencing Projects

  1. Marcus Frohme1,4,
  2. Anamaria A. Camargo2,
  3. Claudia Czink1,
  4. Adriana Y. Matsukuma3,
  5. Andrew J.G. Simpson2,
  6. Jörg D. Hoheisel1, and
  7. Sergio Verjovski-Almeida3
  1. 1Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany; 2Cancer Genetics, Ludwig Institute for Cancer Research, São Paulo, Brazil; 3Departamento de Bioquı́mica, Instituto de Quı́mica, Universidade de São Paulo, São Paulo, Brazil

Abstract

A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of theXylella fastidiosa genome as a test system, we present here an approach to generate, in a directed manner, sequence information from those gaps. We suggest using the complete clone library as a competitor against the genomic DNA of interest in a subtractive hybridization procedure similar to representational difference analysis (RDA). The resulting sequence information can be used to screen selectively other clone resources or serve directly for gap closure.

Footnotes

  • ↵4 Corresponding author.

  • E-MAIL m.frohme{at}dkfz-heidelberg.de; FAX 49-6221-42-4682.

  • Article and publication are at www.genome.org/cgi/doi/10.1101/gr.179401.

    • Received January 8, 2000.
    • Accepted February 27, 2001.
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  1. doi: 10.1101/gr.179401 Genome Res. 11: 901-903 Cold Spring Harbor Laboratory Press

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