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part14 [2009/05/21 11:23]
nuin
part14 [2009/05/21 11:23] (current)
nuin
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We will start comparing the different approaches of the C++ and the Python codes and point out advantages and disadvantages of doing it in one language or the other. First thing we need to do is to count the motifs in all sequences from our foreground and background sets. For the project I was working on, the ideal word length was 10 nucleotides. Basically our C++ approach to increase speed was to transform the character DNA sequences into numbers and then, while sliding a window with the desired word length, hash the base-four numbers into base 10 and increment a vector position, previously initialized with 0. For four nucleotides and a word size of 10 there are 1,048,576 permutations possible, from AAAAAAAAAA to TTTTTTTTTT. Initially the C++ program would do We will start comparing the different approaches of the C++ and the Python codes and point out advantages and disadvantages of doing it in one language or the other. First thing we need to do is to count the motifs in all sequences from our foreground and background sets. For the project I was working on, the ideal word length was 10 nucleotides. Basically our C++ approach to increase speed was to transform the character DNA sequences into numbers and then, while sliding a window with the desired word length, hash the base-four numbers into base 10 and increment a vector position, previously initialized with 0. For four nucleotides and a word size of 10 there are 1,048,576 permutations possible, from AAAAAAAAAA to TTTTTTTTTT. Initially the C++ program would do
-<code c>for(j = 0; j &amp;lt; seqsize; j++)+<code c>for(j = 0; j < seqsize; j++)
{ {
    seqfile.get(base);     seqfile.get(base);
 
part14.txt · Last modified: 2009/05/21 11:23 by nuin
 
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