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Old 02-11-2014, 12:30 AM   #1
Parharn
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Location: Sweden

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Default Annotation and bowtie index difference

Hi,
I am new in the field. Can anybody explain the difference between annotation and index? To me they seem do the same thing, guiding the software to loci in the genome!

Thanks,
Parham
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Old 02-11-2014, 03:05 AM   #2
GenoMax
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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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