The fast way Morten Nielsen BioSys, DTU. The fast algorithm (O2) Database (m) Query (n) Open a gapExtending a gap P Q Affine gap penalties.

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Presentation transcript:

The fast way Morten Nielsen BioSys, DTU

The fast algorithm (O2) Database (m) Query (n) Open a gapExtending a gap P Q Affine gap penalties

The fast algorithm (cont.) Database (m) Query (n) P Q

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

How does it work (D,Q,P, and E-matrices) D Q m n V L I L P V L L P V LI L P V L L P P V LI L P V L L P E V LI L P V L L P

How does it work (D,Q,P, and E-matrices) D Q m n V L I L P V L L P V LI L P V L L P P V LI L P V L L P E V LI L P V L L P

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 V LI L P V L L P V LI L P V L L P V LI L P V L L P