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

Kevin Murphy; Towfique Raj; R. Scott Winters; Peter S. White

doi:10.1093/bioinformatics/btg466

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

Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	588-590
Number of pages	3
Journal	Bioinformatics
Volume	20
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btg466
State	Published - 1 Mar 2004
Externally published	Yes

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title = "me-PCR: A refined ultrafast algorithm for identifying sequence-defined genomic elements",

abstract = "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.",

author = "Kevin Murphy and Towfique Raj and Winters, {R. Scott} and White, {Peter S.}",

note = "Funding Information: The authors gratefully acknowledge G.Schuler for the original e-PCR algorithm and helpful comments. This work was supported in part by NIH grant MH60240.",

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doi = "10.1093/bioinformatics/btg466",

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T2 - A refined ultrafast algorithm for identifying sequence-defined genomic elements

AU - Murphy, Kevin

AU - Raj, Towfique

AU - Winters, R. Scott

AU - White, Peter S.

N1 - Funding Information: The authors gratefully acknowledge G.Schuler for the original e-PCR algorithm and helpful comments. This work was supported in part by NIH grant MH60240.

PY - 2004/3/1

Y1 - 2004/3/1

N2 - 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.

AB - 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.

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

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