suffixarrays

suffixarrays - Sufx Arrays CMSC 858S Sufx Arrays Even...

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SufFx Arrays CMSC 858S
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SufFx Arrays Even though SufFx Trees are O(n) space, the constant hidden by the big-Oh notation is somewhat “big”: 20 bytes / character in good implementations. If you have a 10Gb genome, 20 bytes / character = 200Gb to store your sufFx tree. “Linear” but large. SufFx arrays are a more efFcient way to store the sufFxes that can do most of what sufFx trees can do, but just a bit slower. Slight space vs. time tradeoff.
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Example SufFx Array Idea: lexicographically sort all the sufFxes. Store the starting indices of the sufFxes in an array. s = attcatg$ attcatg$ ttcatg$ tcatg$ catg$ atg$ tg$ g$ $ 1 2 3 4 5 6 7 8 $ atg$ attcatg$ catg$ g$ tcatg$ tg$ ttcatg$ 8 5 1 4 7 3 6 2 sufFx of s index of sufFx sort the sufFxes alphabetically the indices just “come along for the ride”
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Example SufFx Array Idea: lexicographically sort all the sufFxes. Store the starting indices of the sufFxes in an array. s = attcatg$ attcatg$ ttcatg$ tcatg$ catg$ atg$ tg$ g$ $ 1 2 3 4 5 6 7 8 8 5 1 4 7 3 6 2 sufFx of s index of sufFx sort the sufFxes alphabetically the indices just “come along for the ride”
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Another Example SufFx Array Idea: lexicographically sort all the sufFxes. Store the starting indices of the sufFxes in an array. s = cattcat$ cattcat$ attcat$ ttcat$ tcat$ cat$ at$ t$ $ 1 2 3 4 5 6 7 8 $ at$ attcat$ cat$ cattcat$ t$ tcat$ ttcat$ 8 6 2 5 1 7 4 3 sufFx of s index of sufFx sort the sufFxes alphabetically the indices just “come along for the ride”
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Another Example SufFx Array Idea: lexicographically sort all the sufFxes. Store the starting indices of the sufFxes in an array. s = cattcat$ cattcat$ attcat$ ttcat$ tcat$ cat$ at$ t$ $ 1 2 3 4 5 6 7 8 8 6 2 5 1 7 4 3 sufFx of s index of sufFx sort the sufFxes alphabetically the indices just “come along for the ride”
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suffixarrays - Sufx Arrays CMSC 858S Sufx Arrays Even...

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