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Bioinformatics Advance Access originally published online on July 22, 2004
Bioinformatics 2004 20(18):3668-3669; doi:10.1093/bioinformatics/bth413
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

EC_oligos: automated and whole-genome primer design for exons within one or between two genomes

Shaolin Liu 1, Nicholas A. Tinker 2, Stephen J. Molnar 2 and Diane E. Mather 1,*

1 Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Montreal, QC, Canada and 2 Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Central Experimental Farm, Ottawa, ON, Canada

Received on April 26, 2004; revised on July 2, 2004; accepted on July 6, 2004
Advance Access Publication July 22, 2004

Summary: EC_oligos designs oligonucleotides (oligos) from exons of annotated genomic sequence information. It can automatically and rapidly select oligos that are conserved between two sets of sequence data, and can pair up oligos for use as PCR primers. It can do this on a whole-genome scale and according to user-defined criteria.

Availability: The source code, executable program and user manual are available at ftp://ftp.ebi.ac.uk/pub/software/dos/EC_oligos/.

Contact: diane.mather{at}mcgill.ca

* To whom correspondence should be addressed.


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