MATLAB: I have a string of DNA bases and I need to count the number of times I have two identical bases at a certain distance from each other.

dnarepetition

I have a string of DNA bases and I need to count the number of times I have two identical bases at a certain distance from each other. For example- number of times for 'AA', 'AXA', 'AXXA' and so on.. Would love some help with finding the right function.

Best Answer

sum(regexp(yourchararray, 'A[^A]{0,2}A'))

2 being the maximum distance between two A (and 0 the minimum). The regexp says match A followed by 0 to 2 not A, followed by a A.

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MATLAB: Trouble displaying the final count

just do this:

search = 'CAT';
locate = regexp(DNA,search)
count = numel(locate{1}) %number of times CAT appears

edit: it seems like by the time I made the edit above, you accepted my previous answer which i thought was wrong. So i'll just repost it just in case both come in handy:

Prev soln:

sum(contains(DNA,'CAT'))

MATLAB: Take input and use it in a function

Ahmad - please clarify what you mean by it doesn't seem to work. Are you observing an error or are you not getting the correct/desired results?

If I look at the documentation for getgenpept, one of the examples is

 Seq = getgenpept('AAA59174')

and it produces some result. You have even shown that something like

 human = getgenpept('AAA69808','SequenceOnly',true);
 chicken = getgenpept('NP_989750','SequenceOnly',true);

works too. So what is different between the above two statements and your code that gets the input from the user? Note what you are doing

 protein1=input('NCBI accession number  of the first protein: ', 's');
 protein2=input('NCBI accession number  of the second protein: ', 's');

protein1 and protein2 are variables of data type char (so are string variables). With your input example this means that

 protein1 == 'AAA69808'
 protein2 == 'NP_989750'

Now since these are string variables and the first input to the getgenpept is a string variable, there is no need to wrap these variables in quotes like

 seq1 = getgenpept('protein1','SequenceOnly',true);
 seq2 = getgenpept('protein2','SequenceOnly',true);

because if you do, then what you are really passing this function are strings representing the variable name of protein1 or protein2 and not the value of the variable.

Remove the single quotes and change these two lines to

 seq1 = getgenpept(protein1,'SequenceOnly',true);
 seq2 = getgenpept(protein2,'SequenceOnly',true);

Best Answer

Related Solutions

MATLAB: Trouble displaying the final count

MATLAB: Take input and use it in a function

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