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Bioinformatics Vol. 18 no. 3 2002
Pages 484-485
© 2002 Oxford University Press

Applications Notes

Assembly of fingerprint contigs: parallelized FPC

S. R. Ness , W. Terpstra , M. Krzywinski , M. A. Marra and S. J. M. Jones *

Genome Sequence Centre, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada

Received on August 20, 2001 ; revised on October 20, 2001 ; accepted on October 24, 2001

Summary: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest ‘fingerprints’ of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of ‘parallelized FPC’ has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints.

Availability: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.

Contact: fpc{at}bcgsc.bc.ca

* To whom correspondence should be addressed.


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