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Bioinformatics Advance Access originally published online on February 10, 2004
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Bioinformatics 20(8) © Oxford University Press 2004; all rights reserved.

Automated ordering of fingerprinted clones

Stephane Flibotte *, Readman Chiu , Chris Fjell , Martin Krzywinski , Jacqueline E. Schein , Heesun Shin and Marco A. Marra

Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC Canada, V5Z 4E6

Received on April 15, 2003; revised on August 11, 2003; accepted on December 17, 2003
Advance Access Publication February 10, 2004

Motivation: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies.

Results: An algorithm has been developed and implemented to automatically order fingerprinted clones within contigs. The resulting software, named CORAL (Clone ORdering ALgorithm), has been tested on maps that have previously been manually edited and on maps derived from in silico simulations. The fingerprint map and DNA sequence of the human genome has provided an additional test to CORAL. Measurements suggest that CORAL performs significantly better than the software currently used by most laboratories to order fingerprinted clones at throughputs far exceeding those that can be achieved manually.

Availability: Available on request from the authors.

Contact: sflibotte{at}bcgsc.ca

* To whom correspondence should be addressed.


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