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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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