一种DNA的距离定义及其应用

在Watson-Crick的双螺旋模型中,螺旋参数是不变的。例如对B-DNA,螺旋扭角总是36°。近年来,对DNA寡聚体单晶的X光分析表明,螺旋参数将随序列的不同而变化。对于B-DNA,螺旋扭角可在26°—42°之间变化。Dickerson总结出一套规则,可由碱基序列预测螺旋扭角的变化。结果与实验符合甚好。     

绿豆品种的遗传距离估测与聚类分析

通过主成分分析，对50个绿豆品种进行遗传距离分析，并采用多种方法对参试品种进行系统聚类。研究结果表明，以产量、国荚和品质等为代表的6个主成分累计贡献率达87.13%。应用类平均法可将50个品种分成6类，亲本来源与类型划分无必然联系。杂交组合选配时，亲本必须根据性状表现及主成分值综合选择后，在根据遗传距离进行选择，但不宜过分强调遗传距离。研究结果共评出９个理想亲本，分别是港尾选、M004、M041、M058、M094、M097、M112、M123和M133。     

核型似近系数的聚类分析方法

本文根据近年来核型分析所积累的大量资料,以及谭远德(1991)提出的似近分析理论,提出了核型似近系数A聚类分析方法,确定了核型计算公式,井应用于lo种淡水鱼核型似近系数聚类分析,获得了与形态分类学非常一致的结果。此外,还提出了染色体带型计算公式,从而使核型公式和校型似近系数从核型的整体结构、染色体形态结构和染色体内部结构等三个层次上,较精确地刻画了物种核型特性和物种间校型的等同性或同源性。以此核型似近系数作为分类依据所获得的物种分类结果,能真实地和客观地反映物种的自然分类模式。     

绿豆品种的遗传距离估测与聚类分析

通过主成分分析,对50个绿豆品种进行遗传距离分析,并采用多种方法对参试品种进行系统聚类。研究结果表明,以产量、国荚和品质等为代表的6个主成分累计贡献率达87.13%。应用类平均法可将50个品种分成6类,亲本来源与类型划分无必然联系。杂交组合选配时,亲本必须根据性状表现及主成分值综合选择后,在根据遗传距离进行选择,但不宜过分强调遗传距离。研究结果共评出９个理想亲本,分别是港尾选、M004、M041、M058、M094、M097、M112、M123和M133。     

基于负载变化健控理论的线圈耦合系数k的测定

负载变化键控(Load—Shift—Keying)也被称为反射调制^[1]。LSK运用于耦合线圈中次级线圈阻抗的变化能经耦合反射至主线回路并对主线圈回路产生影响这一性质,从而通过调制负载阻抗来实现信号的传递。线圈的耦合系数七是表征线圈间耦合程度的参量。本文在介绍负载变化键控制原理的同时,提出了对实际回路中线圈耦合系数七的测算方法。     

分子生态学重要概念——遗传距离及其测度的理论研究概况

综述了遗传距离的概念、背景,有关遗传距离的几种基本的突变模型以及和遗传距离有关的参量和几种常用统计量,指出在处理蛋白质数据、分子数据以及序列数据时,如何选择相应的统计量和可用的软件包,同时还着重指明了各种模型的假设前提,为处理实际的蛋白质或分子数据时选择合适的模型,和对数据的最终解释提供一些帮助。     

九种蝗虫核型似近系数的聚类分析研究

应用核型似近系数聚类分析方法,研究了小稻蝗Oxya hyla intricata、山稻蝗O.Agav-isa、上海稻蝗O.Shanghaiensis无齿稻蝗O.Adentata、中华稻蝗O.Chisensis、日本稻蝗O.Japonica、短额负蝗Atractomorpha sinensis、奇异负蝗A.Pergrina和日本蚱Tetrix japonica等9种蝗虫的亲缘关系。结果显示,9种蝗虫分为3类：稻蝗,负蝗和蚱。6种稻蝗之间的核型似近系数(λ)在0.961～0.5695之间,2种负蝗的λ＝0.5867,日本蚱与这8种蝗虫的λ在0.5318～.0322。聚类图直观地反映出它们的亲缘关系与形态分类学的分类结果相一致。从9种蝗虫 的核型演化上看,日本蚱是较原始的类型,负蝗分化也较早,而稻蝗则是较进化的类型。     

具有附加信息的一种线性模型的理论

文〔1〕在研究树木材积与胸径或树高的关系时,应用了具有附加信息的一种线性模型（称为随机限制模型）．本文对这种模型从理论上进行了研究,得到了统计量H及τ的分布密度函数,给出了分位数H-α及τ-α的简单近似算法,并证明了其合理性．     

一种预测细胞凋亡蛋白的亚细胞定位的新方法

细胞凋亡蛋白对生物体的发育、维持内环境稳定及人们理解细胞凋亡机制非常重要。文中提出了一种新的蛋白质序列特征提取方法—三肽离散源方法。计算了蛋白质序列中紧邻三联体的出现个数,利用离散增量极小化对凋亡蛋白进行定位预测;同时推广了张春霆等提出的内容平衡精度指数,使其能评估任意类的分类问题。实验结果表明:在凋亡蛋白定位预测研究中,三肽离散源方法在提高总体预测精度的同时,能够较好的解决样本不均衡问题;而内容平衡精度指数能比传统的总体预测精度更准确的评估预测算法的预测能力,有效的反映预测算法对样本不均衡问题的相容能力。     

用38个基因座的基因频率计算中国人群间遗传距离

用 38个基因座的基因频率计算了中国不同省、市、自治区汉族及少数民族相互间的遗传距离 ,并进行了聚类分析 .结果表明 ,中国汉族与少数民族都分为南方蒙古人种与北方蒙古人种两大类型 ,以长江为界 .因此 ,现代人非洲起源说与本地起源说都必须回答这两大类型是何时分开又如何发展而成的问题 .也确凿地从遗传学角度证明各地汉族与当地少数民族血缘相近 ,说明各地汉族中已融入有大量当地少数民族血缘 ,同时 ,各地少数民族也融入了部分汉族血缘 .     

基于蛋白序列的IDQD算法预测蛋白质相互作用

基于蛋白质序列组分信息,提出一个离散增量结合二次判别分析法(IDQD)预测蛋白质相互作用的模型,对人类蛋白质相互作用进行预测.自洽检验的识别精度达到75.89%,3-fold交叉检验的敏感性和特异性分别为64.22%和64.68%.结果表明IDQD算法可以用于蛋白质相互作用的预测.     

中国主要侏罗纪植物群相似性系数的初步研究

选取属级分类单元作为统计变量,Dice系数作为统计公式,对中国早中侏罗世较具代表性的18个植物群进行了相似性的聚类分析.研究结果显示出的区系划分格局在一定程度上支持了前人对植物群时代和性质的判断,同时提出香溪组、万宝组所含植物群的特殊组合与时空因素值得深入研究;中国北方早侏罗世植物群、北方中侏罗世植物群以及南方早中侏罗世植物群三者之间的差异、联系及范围界限需要进一步深入研究.本研究是对古植物学区系研究的有益探索,为中国侏罗纪植物群的大区域系统研究提供了数据基础和参考依据.     

基于多样性指标的分枝杆菌蛋白质亚细胞定位预测

由于蛋白质亚细胞位置与其一级序列存在很强的相关性,利用多样性增量来描述蛋白质之间氨基酸组分和二肽组分的相似程度,采用修正的马氏判别式（这里称为IDQD方法）对分枝杆菌蛋白质的亚细胞位置进行了预测。利用Jackknife检验对不同序列相似度下的蛋白质数据集进行了预测研究,结果显示,当数据集的序列相似度小于等于70％时,算法的预测精度稳定在75％左右。在对整体852条蛋白质的预测成功率达到87．7％,这一结果优于已有算法的预测精度,说明IDQD是一种有效的分枝杆菌蛋白质亚细胞预测方法。     

用离散量的方法识别蛋白质的超二级结构

用离散量的方法,对2208个分辨率在2.5I以上的高精度的蛋白质结构中四类超二级结构进行了识别。从蛋白质一级序列出发,以氨基酸(20种氨基酸加一个空位)和其紧邻关联共同为参数,当序列模式固定长取8个氨基酸残基时,对“822”序列模式3交叉检验的平均预测精度达到78.1%,jack-knife检验的平均预测精度达到76.7%;当序列模式固定长取10个氨基酸残基时,对“1041”序列模式3交叉检验的平均预测精度达到83.1%,jack-knife检验的平均预测精度达到79.8%。     

DNA序列信息的一种新的测度

根据信息理论给出了测度ＤＮＡ序列信息的一种新的方法,获得ＤＮＡ序列４个层次的信息量测度：Ｉｂ,Ｉｆ（１）,Ｉｆ（２）ａｎｄＩｆ（３）,这４种信息测度可分别用来测度ＤＮＡ的碱基序列、密码子序列、编码蛋白质序列和功能蛋白质序列的信息量。从Ｍ．ｅｄｕｌｉｓ的线粒体基因组中两个较短的编码蛋白质的ＤＮＡ序列和使用具有不同倍性的间并密码子组组成的模拟ＤＮＡ序列中所获得计算结果表明,这些信息测度确实能用来揭示所     

Information Theory in Living Systems,Methods, Applications,and Challenges

Living systems are distinguished in nature by their ability to maintain stable, ordered states far from equilibrium. This is despite constant buffeting by thermodynamic forces that, if unopposed, will inevitably increase disorder. Cells maintain a steep transmembrane entropy gradient by continuous application of information that permits cellular components to carry out highly specific tasks that import energy and export entropy. Thus, the study of information storage, flow and utilization is critical for understanding first principles that govern the dynamics of life. Initial biological applications of information theory (IT) used Shannon’s methods to measure the information content in strings of monomers such as genes, RNA, and proteins. Recent work has used bioinformatic and dynamical systems to provide remarkable insights into the topology and dynamics of intracellular information networks. Novel applications of Fisher-, Shannon-, and Kullback–Leibler informations are promoting increased understanding of the mechanisms by which genetic information is converted to work and order. Insights into evolution may be gained by analysis of the the fitness contributions from specific segments of genetic information as well as the optimization process in which the fitness are constrained by the substrate cost for its storage and utilization. Recent IT applications have recognized the possible role of nontraditional information storage structures including lipids and ion gradients as well as information transmission by molecular flux across cell membranes. Many fascinating challenges remain, including defining the intercellular information dynamics of multicellular organisms and the role of disordered information storage and flow in disease.     

Information theoretic perspective on genome clustering

Shannon’s information theoretic perspective of communication helps one to understand the storage and processing of information in one-dimensional sequences. An information theoretic analysis of 937 available completely sequenced prokaryotic genomes and 238 eukaryotic chromosomes is presented. Information content (Id) values were used to cluster these chromosomes. Chargaff’s second parity rule i.e compositional self-complementarity, an empirical fact is observed in all the genomes, except for the proteobacteria Candidatus Hodgkinia cicadicola. High information content, arising out of biased base composition in all the 14 chromosomes of Plasmodium falciparum is found among two other genomes of prokaryotes viz. Buchnera aphidicola str. Cc (Cinara cedri) and Candidatus Carsonella ruddii PV. Despite size and compositional variations, both prokaryotic and eukaryotic genomes do not deviate significantly from an equiprobable and random situation. Eukaryotic chromosomes of an organism tend to have similar informational restraints as seen when a simple distance based method is used to cluster them. In eukaryotes, in certain cases, Id values are also similar for the two arms (p and q arm) of the chromosomes. The results of this current study confirm that the information content can provide insights into the clustering of genomes and the evolution of messaging strategies of the genomes. An efficient and robust Perl CGI standalone tool is created based on this information theory algorithm for the analysis of the whole genomes and is made available at https://github.com/AlagurajVeluchamy/InformationTheory.     

离散增量结合二次判别分析预测人类DNA甲基化位点

DNA甲基化作为直接作用于DNA序列的一种表观遗传修饰,能够在不改变DNA分子一级结构的情况下影响基因表达,在生命活动中扮演着重要的角色.在哺乳动物中,DNA甲基化主要发生在C_pG二核苷酸的胞嘧啶上,并且在基因组中呈现不均匀分布.准确预测DNA甲基化位点有助于阐明DNA甲基化对基因表达的调控作用,并为肿瘤的早期诊断及治疗提供新的依据.本文应用离散增量结合二次判别分析的方法,对人类的C_pG二核苷酸甲基化状态进行了识别.5折交叉检验的整体准确率超过了80%,受试者操作特性曲线面积也达到了0.86.与现有方法相比,预测成功率显著提高.这说明离散增量结合二次判别分析方法适用于甲基化位点的预测;基因组序列中甲基化位点具有序列依赖性.     

Flood Risk Analysis Based on Information Diffusion Theory

Due to the fact that the flood data series of small drainage basins is relatively short, available data are often not sufficient for flood risk analysis. This presents the problem of risk analysis using very small data samples. One method that can be applied is to regard the available small samples as fuzzy information and optimize them using information diffusion technology to yield analytical results with greater reliability. In this article a risk analysis method based on information diffusion theory is applied to create a new flood risk analysis model. Application of the model is illustrated taking the Jinhuajiang and Qujiang drainage basins as examples. This is a new attempt at applying information diffusion theory in flood risk analysis. Computations based on this analytical flood risk model can yield an estimated flood damage value that is relatively accurate. This study indicates that the aforementioned model exhibits fairly stable analytical results, even when using a small set of sample data. The results also indicate that information diffusion technology is highly capable of extracting useful information and therefore improves system recognition accuracy. This method can be easily applied and the analytical results produced are easy to understand. Results are accurate enough to act as a guide in disaster situations.     

Distance decay in an old‐growth neotropical forest

Abstract. Questions: Does distance decay exist in an old‐growth neotropical forest? Is this distance decay stronger than expected due to environmental heterogeneity alone? At what spatial scales are distance decay manifested? Location: La Selva Biological Station, Costa Rica, Central America. Methods: An index of distance decay is applied appropriate for small quadrats (the probability of encountering a conspecific tree) to a grid of 1170 0.01‐ha plots. A null model is provided that accounts for environmental heterogeneity. Results: Significant, but weak, distance decay is found. After correcting for known patterns of environmental heterogeneity, the distance decay almost disappears, except for fine spatial scales. Conclusions: These results are inconsistent with models that predict distance decay at all spatial scales. However, biological processes leading to distance decay may be more relevant and detectable at scales broader than this study. Research utilizing objectively‐located samples over much broader scales is necessary to evaluate the generality and magnitude of distance decay.