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lecture_notes:04-22-2011

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lecture_notes:04-22-2011 [2011/06/09 16:56]
eyliaw
lecture_notes:04-22-2011 [2015/08/09 16:06] (current)
212.129.31.47 ↷ Links adapted because of a move operation
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 ====== Burrows Wheeler Aligner ====== ====== Burrows Wheeler Aligner ======
-We discussed the [[bioinformatic_tools:​bwa]]. ​ It uses the Burrows Wheeler Transform to represent a prefix trie, allowing for short read alignment with mismatches and gaps.+We discussed the [[archive:bioinformatic_tools:​bwa]]. ​ It uses the Burrows Wheeler Transform to represent a prefix trie, allowing for short read alignment with mismatches and gaps.
  
 ===== The prefix trie ====== ===== The prefix trie ======
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 C_X(a) is the number of characters lexicographically before a in X. C_X(a) is the number of characters lexicographically before a in X.
-   0 +   
-   G 1 +   ​L ​2 
-   ​L ​3 +   ​O ​3
-   ​O ​4+
 O_X(a,i) is the number of occurrences of a in B_X[0,i]. O_X(a,i) is the number of occurrences of a in B_X[0,i].
 ^ i ^ B_X[0,i] ^ O_X(G,i) ^ O_X(L,i) ^ O_X(O,i) ^ ^ i ^ B_X[0,i] ^ O_X(G,i) ^ O_X(L,i) ^ O_X(O,i) ^
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 | 6 | LO$OOG ​  | 1        | 1        | 3        |  | 6 | LO$OOG ​  | 1        | 1        | 3        | 
 | 7 | LO$OOGG ​ | 2        | 1        | 3        |  | 7 | LO$OOGG ​ | 2        | 1        | 3        | 
-   +
 There are then two recursive formulas to find the start and end positions of a substring. There are then two recursive formulas to find the start and end positions of a substring.
    End R_(aW) = C(a) + O(a,R_(W) - 1) + 1 or 1 if W is the empty string    End R_(aW) = C(a) + O(a,R_(W) - 1) + 1 or 1 if W is the empty string
-   Start R-(aW) = C(a) + O(a,R-(W)) or n - 1 if W is the empty string+   Start R-(aW) = C(a) + O(a,R-(W)) or (n - 1if W is the empty string
 Where a is the first character and W is the word. Where a is the first character and W is the word.
- 
-To find the end position of the substring GO in  
lecture_notes/04-22-2011.1307663818.txt.gz · Last modified: 2011/06/09 16:56 by eyliaw