Differences

This shows you the differences between two versions of the page.

--- lecture_notes:06-01-2015 [2015/06/01 23:07]
jaredc
+++ lecture_notes:06-01-2015 [2015/06/01 23:15] (current)
jaredc
@@ Line 13: / Line 13: @@
 ===== 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|}}
@@ Line 24: / Line 24: @@
 {{: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]]
@@ Line 116: / Line 120: @@
 [[http://www.ncbi.nlm.nih.gov/pubmed/19451168|BWT paper]]

Banana Slug Genomics