Random amino acid sequence generation with a given amino acid count of a specified sequence

I have a sequence

>sp|Q7RTX1|TS1R1_HUMAN Taste receptor type 1 member 1 OS=Homo sapiens OX=9606 GN=TAS1R1 PE=2 SV=1

MLLCTARLVGLQLLISCCWAFACHSTESSPDFTLPGDYLLAGLFPLHSGCLQVRHRPEVT

LCDRSCSFNEHGYHLFQAMRLGVEEINNSTALLPNITLGYQLYDVCSDSANVYATLRVLS

LPGQHHIELQGDLLHYSPTVLAVIGPDSTNRAATTAALLSPFLVPMISYAASSETLSVKR

QYPSFLRTIPNDKYQVETMVLLLQKFGWTWISLVGSSDDYGQLGVQALENQATGQGICIA

FKDIMPFSAQVGDERMQCLMRHLAQAGATVVVVFSSRQLARVFFESVVLTNLTGKVWVAS

EAWALSRHITGVPGIQRIGMVLGVAIQKRAVPGLKAFEEAYARADKKAPRPCHKGSWCSS

NQLCRECQAFMAHTMPKLKAFSMSSAYNAYRAVYAVAHGLHQLLGCASGACSRGRVYPWQ

LLEQIHKVHFLLHKDTVAFNDNRDPLSSYNIIAWDWNGPKWTFTVLGSSTWSPVQLNINE

TKIQWHGKDNQVPKSVCSSDCLEGHQRVVTGFHHCCFECVPCGAGTFLNKSDLYRCQPCG

KEEWAPEGSQTCFPRTVVFLALREHTSWVLLAANTLLLLLLLGTAGLFAWHLDTPVVRSA

GGRLCFLMLGSLAAGSGSLYGFFGEPTRPACLLRQALFALGFTIFLSCLTVRSFQLIIIF

KFSTKVPTFYHAWVQNHGAGLFVMISSAAQLLICLTWLVVWTPLPAREYQRFPHLVMLEC

TETNSLGFILAFLYNGLLSISAFACSYLGKDLPENYNEAKCVTFSLLFNFVSWIAFFTTA

SVYDGKYLPAANMMAGLSSLSSGFGGYFLPKCYVILCRPDLNSTEHFQASIQDYTRRCGS

T

I wish to get a set of 10000 sequences (in fasta format) having identical amino acid counts as in the above sequence.

I could not use properly the randseq function in getting what I need.

Any help would be highly appreciated.

Answer 1

[Tim DeFreitas]

If you want exactly the same amino acid counts, then you want to randomly shuffle the input sequence, which can be done with randperm:

[~, sequences] = fastaread('pf00002.fa');
targetSeq = sequences{1}; % Select specific sequence from FA file. 
randomSeqs = cell(1,10000);
for i=1:numel(randomSeqs)
    randomSeqs{i} = targetSeq(:, randperm(numel(targetSeq)));
end

Answer 2

[Sam Chak]

Hi @Sk. Hassan

I'm no expert in this, but it is possible to generate a sequence of numbers that associate with the Roman alphabet.

Here is a simple script that you can modify to generate a long sequence of characters like the PASTA spaghetti form.

function amino = generateAmino(n)

ASCII_L = 65;

ASCII_U = 90;

C = round((ASCII_U - ASCII_L).*rand(n, 1) + ASCII_L);

amino = char(C');

end

On the Command Window:

S1 = generateAmino(60)

S1 =

'TGNRWYODEGVGUGXJFGPMJVPOXHTTKOCBNTXDOMAIEUINEPHQRTLCGXEVNZCL'

You can then use a for loop to generate the number of sequences that you want.

numOfSeq = 10000;
for i = 1:numOfSeq
    S(i,:) = generateAmino(60);
end
S

That's the basic idea. You may need to modify the script to select certain Roman alphabets in the ASCII chart.