the number of occurences of each character of one string,in another

i have a string of more than 100 characters (fasta format of a protein sequence. like

'MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH'

which is being shortened here for simplicity) and i want to find out whether or not it is hydrophobic. so i have to check the number of occurrences of each of the characters in the set 'A C F I L M P V W Y'(hydrophob amino acids) in my fasta string. considering the very long length of fasta strings, is there any easy way to do that by matlab string functions?

Answer 1

[Azzi Abdelmalek]

str='MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH'
p={'A' 'C' 'F' 'I' 'L' 'M' 'P' 'V' 'W' 'Y'}'
out=[p cellfun(@(x) nnz(ismember(str,x)),p,'un',0)]

[hiva]

thanks a lot.i guess this works well for a lot of similar cases that are supposed to work the same way in my code(since it is feature extraction and there are lots of features). also tells me how much i don't know from matlab.thanks.

[Stephen23]

This could be simplified and speeded-up by using arrayfun instead of cellfun, and removing the ismember:

>> t = 'ACFILMPVWY';
>> arrayfun(@(x)sum(str==x), t)
ans =
     6     2     4     6    13     2     7     7     1     7

Answer 2

[Peter Perkins]

Another possibility:

>> s = 'MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH';
>> t = 'ACFILMPVWY';
>> n = hist(double(s),1:90);
>> n(t)
ans =
     6     2     4     6    13     2     7     7     1     7

[Jan]

This is a histogram problem, so histc is an efficient and direct solution.

Answer 3

[Luuk van Oosten]

I reckon you are using the BioInformatics Toolbox. In that case you can probably use:

aacount('SEQ')

Where SEQ is of course your sequence of interest: MEQNGLDHDSRSSIDTTINDTQKTFLEF....

and using

nr_A = All.A
nr_C = All.C
nr_F = All.F

etc. (you get the idea)

you get the numbers of your hydrophobic residues. Sum these and you have your hydrophobic score. You might want to 'normalize' this number by dividing this number by the total amount of amino acids in the sequence.

Of course you can write a loop for this and calculate the hydrophobic score for all your sequences in your FASTA file.

Answer 4

[Shoaibur Rahman]

s = 'MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH';
numA = sum(s=='A')
numC = sum(s=='C')
numF = sum(s=='F')
numI = sum(s=='I')
numL = sum(s=='L')
numM = sum(s=='M')
numP = sum(s=='P')
numV = sum(s=='V')
numW = sum(s=='W')
numY = sum(s=='Y')

[hiva]

very simple and delicate. really thanks

Answer 5

[Stephen23]

A neat solution using bsxfun :

>> s = 'MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH';
>> t = 'ACFILMPVWY';
>> sum(bsxfun(@eq,s.',t))
ans =
     6     2     4     6    13     2     7     7     1     7

[hiva]

wow!!! just wonderful. it works pretty well.thanks a lot.