基于对齐的生物序列相似性分析

生物序列相似性(或差异性)分析是生物信息学研究的一种重要的方法。其中基于对齐的生物序列相似性分析方法,重点介绍基于隐马尔可夫模型的比较方法,并比较基于对齐的各种生物序列分析方法的优缺点。     

蛋白质序列的六维表示与相似性分析

给出了蛋白质序列的一种六维表示方法,根据这种表示方法有3种不同表示形式,利用这3种形式来构造距离矩阵的信息熵,然后通过信息熵向量的欧式距离、夹角来比较序列之间的相似性。     

谱分析在DNA序列分析中的应用

目的：谱分析是信号处理的常用方法,其中的统计相关分析、傅里叶变换、小波变换和数字滤波等手段已逐渐应用到DNA序列的分析中,这些应用包括DNA序列的周期性分析、基因识别和同源性分析等方面。本文对谱分析方法在DNA序列分析中的应用情况进行简单的综述。     

高效毛细管电泳在DNA序列分析中的应用

高效毛细管电泳在ＤＮＡ序列分析中的应用种康（兰州大学化学系,兰州７３００００）ＡＰＰＬＩＣＡＴＩＯＮＯＦＨＩＧＨ－ＰＥＲＦＯＲＭＡＮＣＥＣＡＰＩＬＬＡＲＹＥＬＥＣＴＣＴＯＲＨＯＲＥＳＩＳＯＮＤＮＡＳＥＱＵＥＮＣＩＮＧ￥ＣｈｏｎｇＫａｎｇ（Ｄｅｐａｒｔ...     

时间序列的相似性测度

时间序列（time series）是指按时间顺序排列的观测值集合,在生物信息学研究领域中,DNA序列和基因表达数据都可以视为时间序列数据。时间序列分析中很重要的环节就是刻划两个时间序列或者时间子序列的相似性,用于序列比对等。时间序列的相似性测度是时间序列研究中的基础和重点,直接影响查询、聚类等后续计算的效率和精度,在高通量基因芯片数据分析、基因网络构建等研究中,具有重要的应用,目前已引起了众多研究人员的关注,在欧氏距离的基础上进行了大量的研究,本文综述了基于欧式距离和时间弯曲的时间序列相似性测度及其相关领域的研究进展,可作为进一步研究的参考。     

基于DNA拓扑异构酶Ⅱ基因部分序列的侧耳属系统发育分析

对侧耳属（Pleurotus）14个种的14个菌株,亚侧耳属（Hohenbuehelia）1个种和离褶伞属（Lyophyllum）1个种的DNA拓扑异构酶Ⅱ（EC 5．99．1．3）部分序列进行扩增分析。以灰盖鬼伞（Coprinus cinereus）、新型隐球酵母（Cryptococcus neoformans）和玉米黑粉菌（Puccinia polysora）等担子菌为外群,采用最大距离法、最大简约法和最大似然法构建侧耳属的系统发育树。结果表明：作为外群的3个物种独立于所有供试材料;侧耳属菌株作为一大类与供试的离褶伞属和亚侧耳属分开。侧耳属14个种又可细分成6支：可能为侧耳属起源最早的P．flabellatus、P．salmoneostramineus和P．djamor组成一组;P．tuberregium和P．pulmonarius均自成一组;P．abalonus和P．cystidiosus均产生束梗孢,聚为同组;P．eryngii var．eryngii、P．eryngii var．ferulae和P．nebrodensis为一组;另一组由P．ostreatus、P．columbinus、P．cornucopiae和P．citrinopileatus组成。按照侧耳属物种菌丝类型的不同,构建的系统发育树将该属14个种进行系群划分,单、二系菌丝分属于各个不同的分支中,说明单、二系菌丝均为多系起源,与用28S rDNA序列进行系统分析的结果一致。     

基于DNA拓扑异构酶II基因部分序列的侧耳属系统发育分析

对侧耳属（Pleurotus）14个种的14个菌株,亚侧耳属（Hohenbuehelia）1个种和离褶伞属（Lyophyllum）1个种的DNA拓扑异构酶II（EC 5.99.1.3）部分序列进行扩增分析。以灰盖鬼伞（Coprinus cinereus）、新型隐球酵母（Cryptococcus neoformans）和玉米黑粉菌（Puccinia polysora）等担子菌为外群,采用最大距离法、最大简约法和最大似然法构建侧耳属的系统发育树。结果表明：作为外群的三个物种独立于所有供试材料;侧耳属菌株作为一大类与供试的离褶伞属和亚侧耳属分开。侧耳属14个种又可细分成六支：可能为侧耳属起源最早的P. flabellatus、P. salmoneostramineus和P. djamor组成一组;P. tuberregium和P. pulmonarius均自成一组;P. abalonus和P. cystidiosus均产生束梗孢,聚为同组;P. eryngii var. eryngii、P. eryngii var. ferulae和P. nebrodensis为一组;另一组由P. ostreatus、P. columbinus、P. cornucopiae和P. citrinopileatus组成。按照侧耳属物种菌丝类型的不同,构建的系统发育树将该属14个种进行系群划分,单、二系菌丝分属于各个不同的分支中,说明单、二系菌丝均为多系起源,与用28S rDNA序列进行系统分析的结果一致。     

DNA序列分析中的信息熵应用现状

信息熵理论是生物信息学研究的一个重要工具,它在DNA序列分析中有着广泛的应用。本文详细介绍了近年来诸多DNA序列分析问题中信息熵应用的研究进展,并分析了未来该问题的研究方向。     

基于DTW距离的DNA序列相似性分析

在DNA序列相似性的研究中,通常采用的动态规划算法对空位罚分函数缺乏理论依据而带有主观性,从而取得不同的结果,本文提出了一种基于DTW（Dynamic Time Warping,动态时间弯曲）距离的DNA序列相似性度量方法可以解决这一问题．通过DNA序列的图形表示把DNA序列转化为时间序列,然后计算DTW距离来度量序列相似度以表征DNA序列属性,得到能够比较DNA序列相似性度量方法,并用这个方法比较分析了七种东亚钳蝎神经毒素（Buthusmartensi Karsch neurotoxin）基因序列的相似性,验证了该度量方法的有效性和准确性．     

PCR介导的DNA序列系统分析在系统动物学中的应用

ＰＣＲ介导的ＤＮＡ序列系统分析在系统动物学中的应用王亚明，周开亚（南京师范大学生物系南京２１００９７）关键词：ＤＮＡ序列分析，系统发育，系统动物学，分子进化在过去的几十年中，系统学（Ｓｙｓｔｅｍａｔｉｃｓ）研究得到了革命性发展，其原因有三个：首先是基...     

基于3-D图形表示的DNA序列的相似性分析

基于DNA序列的3D图形表示,通过L／L矩阵的规范化最大特征值组成的3维向量来刻画了DNA序列,并基于这种方法,用β-globin基因的第一个外显子分析了11个物种的相似性问题。     

A Novel Method to Analyze the Similarity of Biological Sequences

Abstract

In this paper, we propose a new method based on the 2-D graphical representation to analyze the similarity of biological sequences and classify the protein secondary structure sequences. Instead of computing some characteristics from the distance matrix, the average area surrounded by the curve and X axis is computed as a new invariant. The new method is tested on two sets: the coding sequences of 30 mitochondrial genes from NCBI and 12 protein secondary structure sequences. The similarity/disimilarity and phylogenetic tree (dendrogram) of these sequences verify the validity of our method.     

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Using chaos game representation we introduce a novel and straightforward method for identifying similarities/dissimilarities between DNA sequences of the same type, from different organisms. A matrix is associated to each CGR pattern and the similarities result from the comparison between the matrices of the sequences of interest. Three different methods of analysis of the resulting difference matrix are considered: a 3-dimensional representation giving both local and global information, a numerical characterization by defining an n-letter word similarity measure and a statistical evaluation. The method is illustrated by implementation to the study of albumin nucleotides sequences from eight mammal species taking as reference the human albumin.     

PNN-curve: a new 2D graphical representation of DNA sequences and its application

We introduce a novel 2D graphical representation of DNA sequences based on the pairs of the neighboring nucleotides (PNNs). Then we get the PNNs' distributions and obtain a y-M. The construction of the PNN-curve has some important advantages (1) It avoids loss of information and the PNN-curve standing for DNA sequences does not overlap or intersect with itself. (2) The novel 2D representation is more sensitive. The utility of this method can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of eleven different species in Table 2.     

Enlarged Similarity of Nucleic Acid Sequences

The concept of nucleic acid sequence base alternations is presented.The number of base alterations for the sequences of differentlength is established. The definition of "enlarged similarity"of nucleic acids sequences on the basis of sequence base alterationsis introduced. Mutual information between sequences is usedas a quantitative measure of enlarged similarity for two comparedsequences. The method of mutual information calculation is developedconsidering the correlation of bases in compared sequences.The definitions of correlated similarity and evolution similaritybetween compared sequences are given. Results of the use ofenlarged similarity approach for DNA sequences analysis arediscussed.     

A new 2-D graphical representation of DNA sequences and their numerical characterization

We consider a novel 2-D graphical representation of DNA sequences according to chemical structures of bases, reflecting distribution of bases with different chemical structure, preserving information on sequential adjacency of bases, and allowing numerical characterization. The representation avoids loss of information accompanying alternative 2-D representations in which the curve standing for DNA overlaps and intersects itself. Based on this representation we present a numerical characterization approach by the leading eigenvalues of the matrices associated with the DNA sequences. The utility of the approach is illustrated on the coding sequences of the first exon of human beta-globin gene.     

一种新的蛋白质序列的向量表示方法及其应用

为了更多地挖掘隐藏在蛋白质序列中的信息,本研究将20种氨基酸均匀地排列在单位圆周上,得到每种氨基酸对应的二维坐标,再与氨基酸的6个理化指标结合起来,最终用一个八维向量来刻画蛋白质序列。为避免数据极差对分析结果造成的影响,本研究对蛋白质序列所对应的八维向量作归一化处理。基于归一化后的蛋白质序列的向量表示,运用神经网络对蛋白质序列进行分类,并根据向量之间的欧式距离来量化序列之间的相似性。最后,以9个不同物种的ND5蛋白质序列以及8个不同物种的ND6蛋白质序列为例,Clustal W序列比对方法为基准,对本研究的方法与5-字母方法进行验证和比较,结果表明本研的方法是有效的。     

一种新的RNA二级结构三维图形表示及其应用

本研究提出了一种新的RNA二级结构的图形表示方法,这种方法不同于以往的表示方式。根据所提出的RNA二级结构的图形表示,将对9种病毒的RNA二级结构进行图形表示,构建系统进化树,进行序列间相似性的比较和分析。根据最终结果,可以很清晰地发现,AVII与LRMV两种病毒是最为相似的,另外,较大的距离值出现在了APMV与ALMV;PDV与AVII中,这说明这几种RNA二级结构明显不相似。这一研究结果与前人相似性分析的结果是十分相似的,同时,所采取的方法更加简单易于区分观察且得到的结果又是十分可靠的,因此,这些更加证明了该方法是有效的。     

Alignment-free comparison of genome sequences by a new numerical characterization

In order to compare different genome sequences, an alignment-free method has proposed. First, we presented a new graphical representation of DNA sequences without degeneracy, which is conducive to intuitive comparison of sequences. Then, a new numerical characterization based on the representation was introduced to quantitatively depict the intrinsic nature of genome sequences, and considered as a 10-dimensional vector in the mathematical space. Alignment-free comparison of sequences was performed by computing the distances between vectors of the corresponding numerical characterizations, which define the evolutionary relationship. Two data sets of DNA sequences were constructed to assess the performance on sequence comparison. The results illustrate well validity of the method. The new numerical characterization provides a powerful tool for genome comparison.