the number of occurences of each character of one string,in another
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hiva
am 28 Dez. 2014
Bearbeitet: Luuk van Oosten
am 24 Jan. 2015
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?
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Azzi Abdelmalek
am 28 Dez. 2014
Bearbeitet: Azzi Abdelmalek
am 28 Dez. 2014
str='MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIH'
p={'A' 'C' 'F' 'I' 'L' 'M' 'P' 'V' 'W' 'Y'}'
out=[p cellfun(@(x) nnz(ismember(str,x)),p,'un',0)]
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Peter Perkins
am 29 Dez. 2014
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
1 Kommentar
Luuk van Oosten
am 24 Jan. 2015
Bearbeitet: Luuk van Oosten
am 24 Jan. 2015
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.
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Shoaibur Rahman
am 28 Dez. 2014
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')
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