Paper Info
Title
me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements.
Abstract
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.
Year
DOI
Venue
2004
10.1093/bioinformatics/btg466
Bioinformatics
Keywords
Field
DocType
sequence-defined genomic element,electronic pcr,complex genomes,annotation capability,large genomic element set,refined ultrafast algorithm,expected pcr size input,macintosh platform,large genomes,multithreaded e-pcr,large sequence,iupac nucleotide symbol
Genome,Annotation,Computer science,Algorithm,Genomics,Bioinformatics,Executable
Journal
Volume
Issue
ISSN
20
4
1367-4803
Citations 
PageRank 
References 
2
0.51
0
Authors
4
Name
Order
Citations
PageRank
Michael Kuperberg17589529.66
Towfique Raj220.51
R. Scott Winters3583.14
Peter S White41257.36