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lecture_notes:06-01-2015 [2015/06/01 16:07]
jaredc
lecture_notes:06-01-2015 [2015/06/01 16:15] (current)
jaredc
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 ===== FM Index ===== ===== FM Index =====
  
-For example, the BWT of the string T = "​abracadabra"​ is "​ard$rcaaaabb",​ and here it is represented by the matrix M where each row is a rotation of the text that has been sorted. The transform corresponds to the last column labeled L.+An FM-index is created by first taking the Burrows-Wheeler transform (BWT) of the input text. For example, the BWT of the string T = "​abracadabra"​ is "​ard$rcaaaabb",​ and here it is represented by the matrix M where each row is a rotation of the text that has been sorted. The transform corresponds to the last column labeled L.
  
 {{:​lecture_notes:​screen_shot_2015-06-01_at_3.44.14_pm.png|}} {{:​lecture_notes:​screen_shot_2015-06-01_at_3.44.14_pm.png|}}
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 {{:​lecture_notes:​screen_shot_2015-06-01_at_3.43.33_pm.png|}} {{:​lecture_notes:​screen_shot_2015-06-01_at_3.43.33_pm.png|}}
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 +The program [[http://​bowtie-bio.sourceforge.net/​index.shtml|Bowtie]] uses an FM index technique
 +  * [[http://​www.genomebiology.com/​2009/​10/​3/​R25|Ultrafast and memory-efficient alignment of short DNA sequences to the human genome]]
  
  
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 [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19451168|BWT paper]] [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19451168|BWT paper]]
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lecture_notes/06-01-2015.1433200079.txt.gz ยท Last modified: 2015/06/01 16:07 by jaredc