Author Topic: How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?  (Read 185 times)

mora

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How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?
« on: September 13, 2018, 04:23:27 pm »
Is topology equal to kmers size of the binding site? what if I want to explore kmer sizes > 8?

xiangjun

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Re: How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?
« Reply #1 on: September 13, 2018, 09:00:58 pm »
In the REDUCE Suite, a topology is a shorthand form for exploring a sequence motif, possibly including gaps. It is a flexible and convenient way to test different motif patterns as users see fit in a particular application.

For example, X8 means an 8-mer, with 4^8=65,536 possible combinations of the four canonical DNA or RNA bases. As another example, the topology X3--X4 represents a 7-mer with a 2-nt gap in between. The k-mer size (number of X positions) can be greater than 8: the maximum number is 15. Check the source code for details.

Try the utility program Topo2Dictfile to see a list of sequences corresponding to a given topology. These are the base sequences tested by MotifREDUCE/MatrixREDUCE.

Hope this helps,

Xiang-Jun
« Last Edit: September 13, 2018, 10:32:55 pm by xiangjun »

 

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