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YnkDK / BioSeq-Project2

This project is about implementing and experimenting with pairwise sequence comparison methods to compute optimal global alignments of two sequences where the object is to minimize a cost.
MIT License
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Theoretical Running times #5

Open YnkDK opened 9 years ago

YnkDK commented 9 years ago
  1. A plot showing the running time of global_linear, and a short discussion on whether or not the plot verifies the thereotical running times.
  2. A plot showing the running time of global_affine, and a short discussion on wheter or not the plot verifies the theoretical running and how it compares to the running time of global_linear.
YnkDK commented 9 years ago
  1. To see if they fit theory: Run on different n and m - divide by theoretical bounds and see if we get a horizontal line. Hopefully there is a factor 3 between linear and affine.
  2. To compare the running time, create a ranking box-plot.
YnkDK commented 9 years ago

Example of output of Performance.cpp:

global_linear 100 100 1957169150
global_linear 100 100 1958165151
global_linear 100 100 1956171152
global_linear 100 100 1957169255

i.e. running global_linear with n = 100 and m = 100 which takes just below 2 seconds (time in nanoseconds)