lecture_notes:04-22-2011
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lecture_notes:04-22-2011 [2011/06/09 23:57] eyliaw [Searching] |
lecture_notes:04-22-2011 [2015/08/09 23:06] (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 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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| 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 - 1) if 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/04-22-2011.1307663860.txt.gz · Last modified: 2011/06/09 23:57 by eyliaw
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