04SAAHPCpresentationScalableSystolicArray

5 11 115 12 125 13 135 14 145 15 155 16 165

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Unformatted text preview: 16.5 -17 A -10 -4 -14 -14.5 -15 -15.5 -7 -7.5 -17 -17.5 -18 -18.5 -19 -19.5 -20 -20.5 C -10.5 -14 -8 -9 -9.5 -10 -17 -11 -2.5 -12.5 -13 -13 -22.5 -23 -23.5 -24 G -11 -5.5 -9 -12 -13 -13.5 -14 -21 -12.5 -6.5 -7.5 -17 -8 -17.5 -18 -27.5 G -11.5 -6 -0.5 -10.5 -11 -11.5 -12 -12.5 -13 -13.5 -1.5 -11.5 -12 -3 -12.5 -22 C -12 -6.5 -10 4.5 -5.5 -6 -6.5 -7 -7.5 -8 -8.5 3.5 -6.5 -7 -7 -16.5 T -12.5 -7 -10.5 -5.5 0.5 -9.5 -10 -10.5 -11 -2.5 -12 -6.5 -0.5 -10.5 -11 -2 A -13 -7.5 -11 -6 -9.5 -3.5 -5.5 -5 -14.5 -12.5 -6.5 -16 -10.5 -4.5 -14.5 -12 Score Calculation --- match = 5, mismatch = -4, ogap = -10, egap = -0.5 A -13.5 -8 -11.5 -6.5 -10 -13.5 1.5 -0.5 -9 -13 -16.5 -10.5 -20 -14.5 -8.5 -18.5 C -14 -8.5 -12 -6.5 -1.5 -6 -8.5 -3.5 4.5 -5.5 -6 -6.5 -7 -7.5 -8 -8.5 T -14.5 -9 -12.5 -16 -10.5 -5.5 -9 -12.5 -6.5 9.5 -0.5 -1 -1.5 -2 -2.5 -3 G -15 -9.5 -4 -14 -20 -14.5 -9.5 -13 -7 -0.5 14.5 4.5 4 3.5 3 2.5 5 Backtrack to Produce String Representation A C G G C T _ AA C T G _ _ _ _ _ _ _ G G C C C AAC T G C G G G T S1 S2 G G C C C A A C T G C G G G T 0 V V V V V V V V V V V V V V V A H D V V V V D D D D D D D D D D C H H D D D D H D D V V D D D D D G H D D D D D D H H D D D D D D D G H H D V V V V V V V D V V D D D C H H D D V V V V V V V D V V D D T H H D H D V V V V D D H D V V D A H H D H H D D D D H D D H D V H A H H D H H H D D D H H D D H D V C H H D D D D H D D V V V V V V V T H H D D D D H D H D V V V V V V G H H D V D D H D H H D V V V V V 6 SequenceAlignment Acceleration Score Calculation --- match = 5, mismatch = -4, ogap = -10, egap = -0.5 S1 S2 G G C C C A A C T G C G G G T 0 -10 -10.5 -11 -11.5 -12 -12.5 -13 -13.5 -14 -14.5 -15 -15.5 -16 -16.5 -17 A -10 -4 -14 -14.5 -15 -15.5 C -10.5 -14 -8 -9 -9.5 G -11 -5.5 -9 -12 G -11.5 -6 -0.5 C -12 -6.5 T -12.5 A -13 A -13.5 C -14 T -14.5 G -15 7 Common Hardware Acceleration Techniques q q Ex pl oi t q Construct systolic array of processing elements (PEs) to exploit parallelism Each PE responsible for calculating single column of scoring matrix O(XY) time complexity in software reduced to O(X+Y) in hardware 8 A 0 A G G ... -10 -10.5 -11 ... -10 5 -5 -5.5 ... T -10.5 -5 -1 Pa ra l le lis A -...
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This note was uploaded on 03/27/2012 for the course EEL 4930 taught by Professor Staff during the Spring '08 term at University of Florida.

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