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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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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 - 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 |