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Old 02-11-2014, 03:05 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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Genome Annotation: http://en.wikipedia.org/wiki/Genome_...ome_annotation

Indexing: http://seqanswers.com/forums/showthread.php?t=31498

Bowtie: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010897/
Quote:
Bowtie aligns reads with the aid of an index of the reference genome. The Bowtie index is a refinement of the FM Index (Ferragina and Manzini 2000), which uses the Burrows-Wheeler Transform (Burrows and Wheeler 1994) to achieve both speed and space efficiency
One can create indexes for a genome/reference irrespective of whether or not it is annotated.
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