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--- lecture_notes:06-01-2015 [2015/06/01 20:35]
charles created
+++ lecture_notes:06-01-2015 [2015/06/01 23:15] (current)
jaredc
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+===== Suffix Arrays =====
+Example Suffix Array, A[ ], of "$banana"
+{{:lecture_notes:screen_shot_2015-06-01_at_3.42.20_pm.png|}}
+===== Burrows Wheeler Transform =====
+An example BWT of "^BANANA|"
+{{:lecture_notes:screen_shot_2015-06-01_at_3.41.29_pm.png|}}
+===== FM Index =====
+An FM-index is created by first taking the Burrows-Wheeler transform (BWT) of the input text. For example, the BWT of the string T = "abracadabra" is "ard$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|}}
+ C[c] is a table that, for each character c in the alphabet, contains the number of occurrences of lexically smaller characters in the text.
+{{:lecture_notes:screen_shot_2015-06-01_at_3.43.25_pm.png|}}
+The function Occ(c, k) is the number of occurrences of character c in the prefix L[1..k]
+{{:lecture_notes:screen_shot_2015-06-01_at_3.43.33_pm.png|}}
+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]]
 <code>
 Charles M. - BWT Notes
@@ Line 85: / Line 116: @@
 Additional resources and better examples can be found below:
-{{BWT and FM Index tutorial:http://www.cs.jhu.edu/~langmea/resources/bwt_fm.pdf}}
+[[http://www.cs.jhu.edu/~langmea/resources/bwt_fm.pdf|BWT and FM Index tutorial]]
+[[http://www.ncbi.nlm.nih.gov/pubmed/19451168|BWT paper]]

Banana Slug Genomics

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