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How to construct a for loop to split up a genomic sequence (~5 million nucleotides)?

Asked by artfan100 on 27 Jul 2013

Hi! I'm constructing a script to basically find all promoter sequences in a bacterial genome. Problem is, I can't manage to split up the 5 million base nucleotide genome sequence into manageable segments so I can run seqshoworf command (it only works with max 1 million nucleotides).

here's the code i have so far:

putida = getgenbank('NC_009512.1','SequenceOnly',true);
putida1 = putida(1:100000);
putida2 = putida(100001:200000);
putida3 = putida(200001:300000); %etc
for i=1:1:60
    putida'num2str(i)' = putida(100000*i-99999:100000*i);

Could someone correct the for loop so that I can work separately with each putida(n) segment?


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