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Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.

Applications Note

me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements

Kevin Murphy 1, Towfique Raj 1, R. Scott Winters 1 and Peter S. White 1,2,*

1 Division of Oncology, Children's Hospital of Philadelphia and 2 Department of Pediatrics, University of Pennsylvania, 324 S. 34th Street, Rm 1407 CHOP North, Philadelphia, PA 19104-4318, USA

Received on July 31, 2003 ; revised on August 27, 2003 ; accepted on September 29, 2003
Advance Access Publication January 22, 2004

Summary: We have adapted the originally described electronic PCR (e-PCR) algorithm to perform string searches more accurately and much more rapidly than previously possible. Our implementation [multithreaded e-PCR (me-PCR)] runs sufficiently fast to allow even desktop machines to query quickly large genomes with very large genomic element sets. In addition, me-PCR is multithreaded, interprets all IUPAC nucleotide symbols, allows searches with elements specified by long sequences (such as SNPs), accepts ranges in the expected PCR size input field, requires substantially less memory for analysis of large sequences and corrects a number of minor flaws causing misreporting of hits in exceptional cases. Thus, me-PCR provides increased annotation capabilities for complex genomes to non-expert laboratories.

Availability: me-PCR has been compiled for Linux, Solaris, AIX, Windows and Macintosh platforms. Both source and executable code are freely available to the research community at http://genome.chop.edu/mePCR/

Contact: white{at}genome.chop.edu

* To whom correspondence should be addressed.


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