linspace

# linspace - Space-Efcient Alignment CMSC 858S Space Usage...

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Space-EfFcient Alignment CMSC 858S

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Space Usage O(n 2 ) is pretty low space usage, but for a 10 Gb genome, you’d need a huge amount of memory. Can we use less? Hirschberg’s algorithm
Remember the meaning of a cell 0 1 2 3 4 5 6 7 8 9 10 11 9 8 7 6 5 4 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 x y C A G T T G C A A A A G G T A T G A A T C Best alignment between prefx x[1. .5] and prefx y[1. .5]

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Linear Space for Alignment Scores If you are only interested in the cost or score of an alignment, you need to use only O(n) space. How?
Linear Space for Alignment Scores If you are only interested in the cost or score of an alignment, you need to use only O(n) space. How? 0 1 2 3 4 5 6 7 8 9 10 11 12 9 8 7 6 5 4 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 When Flling in an entry (gray box) we only look at the current and previous rows. Only need to keep those two rows in memory.

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We can do more. .. Given 2 strings X and Y, we can, in linear space and O(nm) time, compute the cost of aligning. .. every preFx of X with Y X with every preFx of Y a particular preFx of X with every preFx of Y a particular sufFx of X with every sufFx of Y How can we do that?
Best Alignment Between Prefx oF X and Y 0 1 2 3 4 5 6 7 8 9 10 11 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 1g 2g 3g 4g 5g 6g 7g 8g 9g 10g 11g 12g x y C A G T T G C A A A A G G T A T G A A T C Score of an optimal alignment between Y and a preFx of X

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Fill in the matrix by columns. .. 0 1 2 3 4 5 6 7 8 9 10 11 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 1g 2g 3g 4g 5g 6g 7g 8g 9g 10g 11g 12g x y C A G T T G C A A A A G G T A T G A A T C What is this column?
Fill in the matrix by columns. .. 0 1 2 3 4 5 6 7 8 9 10 11 9 8 7 6 5 4 3 2 1 0 9g 8g 7g 6g 5g 4g 3g 2g 1g 0 1g 2g 3g 4g 5g 6g 7g 8g 9g 10g 11g 12g x y C A G T T G C A A A A G G T A T G A A T C What is this column?

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## linspace - Space-Efcient Alignment CMSC 858S Space Usage...

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