DNA序列检测源码程序 - matlab算法设计

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标题：DNA序列检测源码程序
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所属分类: 算法设计资源类型：文件大小: 14.76 KB 上传时间: 2016-01-25 19:41:27 下载次数: 6 资源积分：1分提供者: xiaopeng2 DNA序列检测源码程序

内容：
DNA序列检测源码程序，程序员在编程的过程中可以参考学习使用，希望对IT程序员有用，此源码程序简单易懂、方便阅读，有很好的学习价值！

% ------------------------------------------------------------------ %

% -------------- Prepared by : Ismail M. El-Badawy ----------------- %

% ------------------------------------------------------------------ %

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% This code reads the F56F11.4 dna sequence and detect the period-3 %

% -------- behavior using singular value decomposition with -------- %

% ---------- frame size 'frmsz' to predict the locations ----------- %

% --------------- of protein-coding regions (exons) ---------------- %

% ---------------------- in the dna sequence ----------------------- %

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% This code is a simulation of the method proposed in the following paper:

% M. Akhtar, E. Ambikairajah, and J. Epps, 揇etection of period-3

% behavior in genomic sequences using singular value decomposition,?

% in Proc. IEEE Int. Conf. Emerging Technologies, 2005, pp. 13?7.

clear all;close all;clc

% Read dna sequence from FASTA format file downloaded from http://www.ncbi.nlm.nih.gov/ %

% ------------------------------------------------------------------------------------- %

sample_dna = fastaread('sequence_AF099922.fasta'); % Caenorhabditis elegans (Wormbase)

% Convert the sequence from structure array to string %

% --------------------------------------------------- %

sample_dna = struct2cell(sample_dna);

sample_dna = cell2mat(sample_dna(2));

% Take only the F56F11.4 sequence (positions from 7021 to 15020) %

% -------------------------------------------------------------- %

sample_dna = sample_dna(7021:15020);

% Actual locations of coding sequences (cds or exons) %

% --------------------------------------------------- %

cds = [928 1038 2527 2856 4113 4376 5464 5643 7254 7604];

for ctr = 1:2:length(cds)

actual_exons(cds(ctr):cds(ctr+1)) = 1;

end

actual_exons(cds(length(cds))+1:length(sample_dna)) = 0;

% Define the frame size for singular value decomposition (svd) %

% ------------------------------------------------------------ %

frmsz = 81;

if mod(frmsz,3) ~= 0

error('Frame size should be a multiple of 3')

end

% Convert string to numerical values (Binary Indicator Sequences) %

% --------------------------------------------------------------- %

[xA xT xC xG] = dna_binary(sample_dna);

xA = [zeros(1,floor(frmsz/2)) xA zeros(1,ceil(frmsz/2))]; % Zero padding from both sides

xT = [zeros(1,floor(frmsz/2)) xT zeros(1,ceil(frmsz/2))];

xC = [zeros(1,floor(frmsz/2)) xC zeros(1,ceil(frmsz/2))];

xG = [zeros(1,floor(frmsz/2)) xG zeros(1,ceil(frmsz/2))];

% Anti-notch Filter centered at angular frequency 2pi/3 %

% ----------------------------------------------------- %

R = 0.992;

theta = (2*pi)/3;

% Filter Coefficients %

% ------------------- %

b = [1 0 -1];

a = [1 -2*R*cos(theta) R^2];

% Filtering the signal (DNA Sequence) %

% ----------------------------------- %

uA = filter(b,a,xA);

uT = filter(b,a,xT);

uC = filter(b,a,xC);

uG = filter(b,a,xG);

% Detection of Period-3 Behavior using Singular Value Decomposition %

% ----------------------------------------------------------------- %

for n = 1:length(sample_dna)

sa = reshape(uA(n:n+frmsz-1),3,frmsz/3);

XA(n) = max(svd(sa));

st = reshape(uT(n:n+frmsz-1),3,frmsz/3);

XT(n) = max(svd(st));

sc = reshape(uC(n:n+frmsz-1),3,frmsz/3);

XC(n) = max(svd(sc));

sg = reshape(uG(n:n+frmsz-1),3,frmsz/3);

XG(n) = max(svd(sg));

end

X = XA + XT + XC + XG;

% Plot X Vs nucleotide positions %

% ------------------------------- %

plot(X/max(X))

hold on;

plot(actual_exons,':k','linewidth',1) % Show actual exonic regions

axis([0 8000 0 1.05])

xlabel('DNA Sequence (Nucleotide Position)')

ylabel('SVD')

title('Detection of Period-3 Behavior using SVD')

文件列表（点击上边下载按钮，如果是垃圾文件请在下面评价差评或者投诉）:

DNA序列检测源码程序/
DNA序列检测源码程序/SVD/
DNA序列检测源码程序/SVD/dna_binary.m
DNA序列检测源码程序/SVD/main.m
DNA序列检测源码程序/SVD/sequence_AF099922.fasta

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