基于DNA计算的RNA序列多点“突变”与首段碱基的数字编码及其运算法则

RNA序列的高维空间二进制编码有以下优点:除可以对RNA序列的碱基结构、功能基团、碱基互补、氢键强弱等性质进行编码之外,还可方便的进行数学与逻辑运算。该文研究了RNA序列高维空间数字编码的更一般、更深刻的运算法则:(1)进一步研究RNA序列高维空间的表观维数NV,数值维数NX以及差异维数Nd,具体刻给出了当Nd=0,1,2,2n或2n+1(n=0,1,2,…)时,RNA序列的首段碱基及其数值取值范围。(2)推导出RNA序列多点“突变”(单核苷酸多态性SPN)的运算法则,将以前的结果推广到一般情形,深刻探讨了RNA序列之汉明距离、汉明值的变化及其数值变化情况。(3)利用RNA序列的定值部Xi和定位部Wi及其计算公式,从新的角度导出RNA重复序列的编码法则和运算法则,进而统一了以前的结果。     

基于聚类小生境遗传算法的DNA编码优化

DNA编码优化问题是DNA计算中的核心问题。分析DNA编码优化的约束条件,在单链DNA序列集合上引入h距离,将聚类小生境技术应用于小种群遗传算法的构造,对DNA编码优化问题进行求解。基于h距离定义DNA序列间的相似函数,将碱基字母编码为4进制整数、DNA编码序列作为个体编码为4进制整数向量、种群编码为4进制整数矩阵,基于模4算术运算,构造相应的遗传算子,并给出DNA编码序列的具体计算结果。实验结果表明,与现有DNA编码序列优化结果相比,该算法可得到更好的DNA编码序列且计算效率较高。     

信息熵动态变异概率RNA遗传算法

约束优化问题是科学研究和工程应用的热点和难点.受生物RNA分子遗传信息表达机制和信息熵概念的启发,本文提出了一种信息熵动态变异概率RNA遗传算法来求解这类问题,算法采用碱基序列的个体编码方式,并用RNA分子再编码和蛋白质折叠操作代替传统遗传算法的交叉操作,在变异概率的设置中,借鉴信息熵对系统有序程度度量的概念,根据当前种群个体每一位的碱基分布情况对变异概率进行自适应调整.测试函数的仿真结果表明所提出的算法具有收敛速度快、搜索精度高的特点.将该算法用于求解短期汽油调合调度问题,能得到比其他几种算法更高的调合利润.     

基于SDNA-GA 优化的模糊神经网络控制

针对最新的生物DNA研究,病毒中同一DNA碱基顺序可以编码出2条或者3条不同的多肽链.在此基础上分析与模仿了重叠基因和重叠密码的机理,得到一种新的基于重叠基因编码框架,从而提高了问题求解的效率;同时,得到一种移码解读框架的DNA遗传算法(SDNA-GA)计算模型,并将其应用于一类广义隶属度型T-S模糊神经网络控制器(GTS-FNNC)的优化设计,实现了GTS-FNNC的在线学习.     

以DNA为载体的信息隐藏方法研究

提出一种新的在DNA和RNA中隐藏信息的方法,以此可以保护基因的新发现、基因治疗药物等的知识产权.该方法综合了密码子冗余和算术编码,在DNA活跃的译码部分进行信息隐藏而不改变最终的氨基酸序列.     

一种新的D NA序列图形表达的方法

针对当前DNA序列图形表达模式中存在简并现象的相关问题,提出了一种新的二元符号图形表达方式。将四类碱基的编码过程看成是构成DNA序列的元素在直角坐标平面上的移动过程,以两种不同的标志符号来解决可能出现的元素重叠情况。此方案所标志的图形不存在自交现象,从而在DNA序列和图形表达之间建立了一一对应的关系。通过实例说明该方法在对无向图和有向图表达中均能有效地降低图形简并度,并引入人工代谢系统中的编码模式作为分析工具对DNA序列进行比较分析;以代谢中间物值作为参数,研究不同物种的DNA序列之间的相似性。实例分析表明,该参数能较好地表征不同物种之间的相似性程度高低,是一种简便可行的DNA序列特征的比较方法。     

几种大黄蒽醌类化合物光敏性的量子化学计算

采用密度泛函方法,研究了大黄中几种蒽醌类化合物与氧分子以及DNA和RNA碱基之间的光敏反应。所有的激发态计算包括垂直激发能采用的都是含时密度泛函方法(TD.DFT)。计算结果表明:有氧条件下,大黄蒽醌类化合物在真空和溶剂中都能产生单重态氧~1O_2,而只有在水溶液中才能产生超氧负离子自由基O_2~(*-)无氧条件下,在水和乙醚溶剂中,大黄蒽醌类化合物可以损害DNA和RNA。     

利用DNA遗传算法求解Flow-Shop调度问题

由于经典遗传算法在求解调度问题尤其是处理复杂的、混淆的和多任务问题时不够灵活且计算速度慢,论文引入DNA技术借助生物学理论对其进行改进。DNA遗传算法继承了遗传算法全局搜索的能力,同时利用DNA双螺旋结构和碱基互补配对原则进行编码运算,提高了算法的有效性和收敛速度,从而很好地解决了NP-hard性质的Flow-Shop调度问题。     

基于DNA遗传算法的曲面最短路径问题

DNA遗传算法采用遗传算法的整体结构，借助生物学DNA技术，利用DNA双螺旋结构和碱基互补配对原则进行编码运算，继承了遗传算法全局搜索的能力，提高了算法的有效性和收敛速度，避免了经典的遗传算法容易出现的“早熟收敛”和“收敛速度慢”的难题，求解了曲面最短路径规划问题。数值仿真实例证明了该算法的有效性和实用性。     

将DNA碱基翻译成蛋白质氨基酸程序设计

基因是生物的遗传物质,蛋白质是生物性状的体现物质,基因通过控制蛋白质的形成来控制生物的性状。根据DNA转录形成RNA,RNA翻译形成蛋白质的规则,利用C语言编写出翻译基因碱基序列成蛋白质氨基酸序列的程序,这无论在遗传学、医学研究,还是C语言程序设计的教学和学习都具有一定的实用价值。     

Homology modeling,molecular dynamics,and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)

The ability to repair DNA is important for the conservation of genetic information of living organisms. Cells have a number of ways to restore damaged DNA, such as direct DNA repair, base excision repair, and nucleotide excision repair. One of the proteins that can perform direct repair of DNA bases is Escherichia coli AlkB. In humans, there are 9 identified AlkB homologs, including AlkB homolog 1 (ALKBH1). Many of these proteins catalyze the direct oxidative dealkylation of DNA and RNA bases and, as such, have an important role in repairing DNA from damage induced by alkylating agents. In addition to the dealkylase activity, ALKBH1 can also function as an apyrimidinic/apurinic lyase and was proposed to have a distinct lyase active site. To our knowledge, no crystal structure or complete homology model of ALKBH1 protein is available. In this study, we have used homology modeling to predict the structure of ALKBH1 based on AlkB and Duffy-binding-like domain crystal structures as templates. Molecular dynamics simulations were subsequently performed on the predicted structure of ALKBH1. The positions of two disulfide bonds or a zinc-finger motif and a disulfide bond were predicted and the importance of these features was tested by mutagenesis. Possible locations for the lyase active site are proposed based on the analysis of our predicted structures and previous experimental results.     

A generic algorithm for finding restriction sites within DNA sequences

This paper describes a generic algorithm for finding restriction sites within DNA sequences. The 'genericity' of the algorithm is made possible through the use of set theory. Basic elements of DNA sequences, i.e. nucleotides (bases), are represented in sets, and DNA sequences, whether specific, ambiguous or even protein-coding, are represented as sequences of those sets. The set intersection operation demonstrates its ability to perform pattern-matching correctly on various DNA sequences. The performance analysis showed that the degree of complexity of the pattern matching is reduced from exponential to linear. An example is given to show the actual and potential restriction sites, derived by the generic algorithm, in the DNA sequence template coding for a synthetic calmodulin.     

Image encryption using DNA complementary rule and chaotic maps

This paper proposes a novel confusion and diffusion method for image encryption. One innovation is to confuse the pixels by transforming the nucleotide into its base pair for random times, the other is to generate the new keys according to the plain image and the common keys, which can make the initial conditions of the chaotic maps change automatically in every encryption process. For any size of the original grayscale image, after being permuted the rows and columns respectively by the arrays generated by piecewise linear chaotic map (PWLCM), each pixel of the original image is encoded into four nucleotides by the deoxyribonucleic acid (DNA) coding, then each nucleotide is transformed into its base pair for random time(s) using the complementary rule, the times is generated by Chebyshev maps. Experiment results and security analysis show that the scheme can not only achieve good encryption result, but also the key space is large enough to resist against common attacks.     

A dynamic representation-based,de novo method for protein-coding region prediction and biological information detection

In this paper, we propose a new method for the prediction of protein coding regions that is designed to detect novel genes that do not have known, close homologs. The proposed method uses a dynamic representation scheme to convert DNA sequences into a numerical form, and then it uses the nucleotide distribution variance to calculate the period-3 spectrum. The dynamic representation scheme assigns numerical pairs to the nucleotides to emphasize the effect of the nucleotides that have a stronger participation in the period-3 spectrum. The proposed method also uses the nucleotide distribution variance which has less computational cost than the Fourier transform to extract the period-3 spectrum. A post-processing of the period-3 spectrum signal is performed to smooth the signal, detect the period-3 spectrum peaks, and locate the boundaries of the protein-coding regions.The analysis of the receiver operating characteristic (ROC) curves shows that the proposed method outperforms other Digital Signal Processing (DSP)-based methods. The analysis of the false positive peaks shows that these regions have a similarity with regions that have functional patterns in other DNA sequences. The method also highlights and explores the capabilities of techniques that perform better than homology-based techniques for de novo protein prediction. We believe that this is an area of research that has been underemphasized and deserves additional attention.     

DNA一级序列不同编码方法和相似度比较

为了DNA一级序列的相似度计算,本文比较了三种编码方案:单一碱基在DNA序列中的相对位置、二联码即相邻二碱基在序列中的相对位置、编序单一碱基在DNA序列中的相对位置和二联码在序列中的编序相对位置,在此基础上,运用分子连接性指数计算得到序列的不变量,进而,由塔尼莫特法计算得到物种间的相似度。由单一碱基在DNA序列中的相对位置法比较相似度,对于本研究中10个物种,得到了与生物进化树非常相一致的结果。     

基于弹性网和直方图相交的非负局部稀疏编码

针对稀疏编码模型在字典基的选择时忽略了群效应,且欧氏距离不能有效度量特征与字典基之间距离的问题,提出基于弹性网和直方图相交的非负局部稀疏编码方法（EH-NLSC）。首先,在优化函数中引入弹性网模型,消除字典基选择数目的限制,能够选择多组相关特征而排除冗余特征,提高了编码的判别性和有效性。然后,在局部性约束中引入直方图相交,重新定义特征与字典基之间的距离,确保相似的特征可以共享其局部的基。最后采用多类线性支持向量机进行分类。在4个公共数据集上的实验结果表明,与局部线性约束的编码算法（LLC）和基于非负弹性网的稀疏编码算法（NENSC）相比,EH-NLSC的分类准确率分别平均提升了10个百分点和9个百分点,充分体现了其在图像表示和分类中的有效性。