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The fast way Morten Nielsen BioSys, DTU
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The fast algorithm (O2) Database (m) Query (n) Open a gapExtending a gap P Q Affine gap penalties
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The fast algorithm (cont.) Database (m) Query (n) P Q
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The fast algorithm (cont.) Database (m) Query (n) P Q eij = 1 match eij = 2 gap-opening database eij = 3 gap-extension database eij = 4 gap-opening query eij = 5 gap-extension query E14523E14523
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How does it work (D,Q,P, and E-matrices) D Q m n V L I L P V L L P 0 0 0 0 000000 V LI L P V L L P 10 0 0 0 0 000000 P V LI L P V L L P 0 0 0 0 000000 E V LI L P V L L P 1 0 0 0 0 000000
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How does it work (D,Q,P, and E-matrices) D Q m n V L I L P V L L P 0 0 0 0 000000 V LI L P V L L P 5 10 0 0 0 0 000000 P V LI L P V L L P 5 0 0 0 0 000000 E V LI L P V L L P 4 1 0 0 0 0 000000
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How does it work (D,Q,P, and E-matrices) D Q P m n E 11 V L I L P V L L P 101293 845104 2-205 0 0 0 0 0 000000 1 V LI L P V L L P 1133 51113 51412 55541 0 0 0 0 000000 18 V LI L P V L L P 14930 11125 89100 2345 0 0 0 0 000000 20 V LI L P V L L P 181493 111517104 89 155 234510 0 0 0 0 000000
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