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Old 02-25-2011, 11:20 AM   #1
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Default PubMed: PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.

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PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.

AMIA Summits Transl Sci Proc. 2010;2010:25-9

Authors: Pitzer E, Kim J, Patel K, Galante PA, Ohno-Machado L

Microarray probes and reads from massively parallel sequencing technologies are two most widely used genomic tags for a transcriptome study. Names and underlying technologies might differ, but expression technologies share a common objective-to obtain mRNA abundance values at the gene level, with high sensitivity and specificity. However, the initial tag annotation becomes obsolete as more insight is gained into biological references (genome, transcriptome, SNP, etc.). While novel alignment algorithms for short reads are being released every month, solutions for rapid annotation of tags are rare. We have developed a generic matching algorithm that uses genomic positions for rapid custom-annotation of tags with a time complexity O(nlogn). We demonstrate our algorithm on the custom annotation of Illumina massively parallel sequencing reads and Affymetrix microarray probes and identification of alternatively spliced regions.

PMID: 21347141 [PubMed - in process]



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Old 02-28-2011, 08:00 AM   #2
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http://dbmi.ucsd.edu/confluence/disp...onMatcher/Home
appears to be the source code URL, though it is cryptic; this should show up in the wiki soon
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