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。     

小波变换与生物医学信号处理

作为数字信号处理领域的一个重要分支,生物医学信号处理理论与技术的研究一直受到国内外科技工作者的高度重视。小波变换是近年来发展起来的一种新的信号分析工具。本文结合生物医学信号与小波变换的特点,探讨了小波变换在生物医学信号处理领域的应用前景。     

面向蛋白质功能位点识别的机器学习平台构建

有关蛋白质功能的研究是解析生命奥秘的基础,机器学习技术在该领域已有广泛应用。利用支持向量机(support vectormachine,SVM)方法,构建一个预测蛋白质功能位点的通用平台。该平台先提取非同源蛋白质序列,再对这些序列进行特征编码(包括序列的基本信息、物化特征、结构信息及序列保守性特征等),以编码好的样本作为训练数据,利用SVM进行训练,得到敏感性、特异性、Matthew相关系数、准确率及ROC曲线等评价指标,反复测试,得到评价指标最优的SVM模型后,便可以用来预测蛋白质序列上的功能位点。该平台除了应用在预测蛋白质功能位点之外,还可以应用于疾病相关单核苷酸多态性(SNP)预测分析、预测蛋白质结构域分析、生物分子间的相互作用等。     

基于小波变换心电信号消噪方法研究

小波变换是近年来兴起的热门信号处理技术,是一种非常有用的信号处理工具。本文阐述了连续小波去噪和离散小波去噪的原理,分析了基于小波去噪的几种不同方法（其中包括小波分解与重构,小波变换阈值法,小波变换模极大值法,以及它与独立分量分析相结合去除噪声的方法等）。通过检测和验证,表明该方法能较好的实现心电信号的消噪,都取得了较好的效果;同时,比较了每种方法的不足和缺陷。基于小波变换心电信号消噪的研究进展较快,通过多种方法结合运用进行消噪并取得了很好的效果,展望了利用基于小波变换心电信号消噪的前景。     

小波分析在生态环境研究中的应用初探

小波分析(Wavelet Analysis)是时间-频率分析领域近年来迅速发展的一种新技术,具有多时间尺度,多层次和多分辨的特性,已被广泛地应用在信号分析、信息分析和地球科学研究上.本文以大亚湾大鹏澳水域2002年春秋两季浮游植物30d连续观测资料为例,首次运用小波技术分析浮游植物对生境变化的响应特征.结果表明,通过小波变换的浮游植物数量(细胞密度)的时间序列,存在各自的优势周期和多时间尺度结构特征,而春秋两季浮游植物细胞密度的优势周期和多时间尺度结构,在大尺度上大致相同,但在小尺度结构上稍有差别;使用不同小波变换(如Mexh小波变换和Morlet小波变换)可以取得各自不同特点的结果.本文对小波分析技术在生态环境研究的初步应用说明,小波分析技术可以对生态系统中浮游植物的动态变化进行多时间尺度,多层次和多分辨的分析,为深入研究和预测浮游植物的动态变化提供一种新的分析手段.     

基于功率谱的流感病毒蛋白质序列结构分析

基于经典HP模型,本文采用离散傅里叶变换获取蛋白质特征,利用分层聚类方法进行蛋白质序列的结构分析。其目的是将自动信号频谱分析技术与层次聚类方法相结合,并应用到蛋白质序列结构分析中。通过流感病毒HA和NA蛋白质序列的实验结果表明:应用该方法可得到非常好的分类结果。这些研究为基于大数据的蛋白质序列的自动信息提取和结构分析提供基础。     

利用小波变换的一种快速预测基因方法

三周期性是大多数基因组序列的编码区所具有的主要特征.本文提出只计算1/3频率点的傅里叶频谱的快速计算方法,并用它分析DNA序列的三周期性,再利用小波变换在一定尺度下滤波来实现对DNA序列编码区的预测.理论分析和大量计算机实验证实了方法的有效性,预测效果良好.该方法运算快速,不需要任何训练组,也不依赖于现有数据库的信息.     

基于统计模型的基因预测

基因预测是指预测DNA序列中编码蛋白质的部分。随着多数生物基因组的测序工作的完成 ,基因预测更显得尤为重要。基因预测主要包括两种方法 ,首先是同源方法 ,也称为“外在方法” ,其次是基因预测方法或称为“内在方法”。主要对隐马尔可夫模型、傅立叶变换、动态规划等几种“外在方法”进行介绍。     

园艺植物分子育种相关生物信息资源及其应用

园艺植物分子育种中, 生物信息技术是一项新技术。GenBank、EMBL、DDBJ、Swiss-Prot等数据库及其序列查询系统、序列比对软件和序列提交软件是园艺植物分子育种中的重要生物信息资源。本文综述了这些生物信息资源, 以及它们在克隆新基因、预测新序列功能、鉴定种质资源和进行系谱分析等方面的应用。     

EST分析技术在鸡基因组学研究中的应用

表达序列标签（EST）是由大量随机取出的cDNA库克隆经测序得到的组织或细胞基因组的一段cDNA序列,一个EST代表生物体某种组织某一时期的一个表达基因。综述了EST分析技术在鸡基因组研究中的应用。如用于鉴定、发现和预测鸡的新基因,用于基因图谱的绘制,用于筛选基因的单核苷酸多态性（SNP）位点,用于基因表达分析和基因芯片制作等。EST数据库和生物信息学的联合分析技术在推动家鸡后基因组的研究中发挥着重要的作用。     

体内直接克隆大片段DNA的研究进展

基因组序列的功能分析以及代谢途径的构建改造等都需要克隆目的DNA。获得大片段DNA序列的方法有构建和筛选基因文库,PCR扩增,体外大片段DNA合成和组装等,但体内重组直接克隆的方法在操作、克隆长片段和应用等方面更具优势。介绍了Red/ET重组介导的大片段DNA体内直接克隆的主要方法及其应用。     

Proteomics meets microbiology: technical advances in the global mapping of protein expression and function

The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques that have made a significant impact on the resolution of complex proteomes. In addition, we highlight recent developments in the field of chemical proteomics, a branch of proteomics aimed at functionally profiling a proteome. These techniques include the development of activity-based probes and activity-based protein profiling methods as well as the use of synthetic small molecule libraries to screen for pharmacological tools to perturb basic biological processes. This review will focus on the applications of these technologies to the field of microbiology.     

Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem

MOTIVATION: One of the main tasks of DNA sequence analysis is identification of repetitive patterns. DNA symbol repetitions play a key role in a number of applications, including prediction of gene and exon locations, identification of diseases, reconstruction of human evolutionary history and DNA forensics. RESULTS: A new approach towards identification of tandem repeats in DNA sequences is proposed. The approach is a refinement of previously considered method, based on the complex periodicity transform. The refinement is obtained, among others, by mapping of DNA symbols to pure quaternions. This mapping results in an enhanced, symbol-balanced sensitivity of the transform to DNA patterns, and an unambiguous threshold selection criterion. Computational efficiency of the transform is further improved, and coupling of the computation with the period value is removed, thereby facilitating parallel implementation of the algorithm. Additionally, a post-processing stage is inserted into the algorithm, enabling unambiguous display of results in a convenient graphical format. Comparison of the quaternionic periodicity transform with two well-known pattern detection techniques shows that the new approach is competitive with these two techniques in detection of exact and approximate repeats.     

FTICR mass spectrometry for qualitative and quantitative bioanalyses

Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is playing an increasing role in the characterization of cellular systems owing to its capabilities for providing higher confidence of identification, increased dynamic range and sensitivity unmatched by other MS platforms. Particularly in proteomics, where global and quantitative approaches are essential, the attributes of FTICR-MS are poised to make significant contributions. Recent advances in the field that have particular importance for proteomic applications include the use of high-performance micro-capillary column separation techniques coupled to FTICR, as well as methods that improve protein identification, sensitivity, dynamic range and throughput.     

Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations

Species-specific enumeration of mixed community is invaluable as it facilitates a better understanding of the significance of the individual strains, their interactions, and the underlying mechanisms of community dynamics. Mixed microbial community has been characterized by microbiological, biochemical, or molecular biology-based methods. While microbiological and biochemical techniques do not provide adequate quantitative information of the members of the consortia and require additional techniques for a more comprehensive analysis, molecular biology-based methods analyze the microbial consortium based on specific DNA sequences and do not require isolation and culturing of bacteria for quantitative analysis. These methods outshine conventional culture-based techniques in terms of better sensitivity, reproducibility, and reliability. Quantitative molecular biology methods have been classified as PCR-based and probe hybridization methods. The PCR-based methods includes quantitative real-time PCR and terminal restriction fragment length polymorphism, while fluorescent in situ hybridization and DNA microarrays fall under probe hybridization methods. The workflow, the quantification methods, and their potential applications are discussed in this review by highlighting their advantages and possible limitations.     

Genome comparisons and analysis

As we enter the post-genomic era, with the accelerating availability of complete genome sequences, new theoretical approaches and new experimental techniques, our ability to dissect cellular processes at the molecular level continues to expand. Recent advances include the application of RNA interference methods to characterize loss-of-function phenotype genes in higher eukaryotes, comparative analysis of the human and mouse genome sequences, and methods for reconciling contradictory phylogenetic reconstructions. New developments feed into the increasingly rich content of databases such as the COG database. The next phase of research will be increasingly dominated by efforts to integrate the deluge of data into our understanding of biological systems.     

Locating probable genes using Fourier transform approach

FTG is a web server for analyzing nucleotide sequences to predict the genes using Fourier transform techniques. This server implements the existing Fourier transform algorithms for gene prediction and allows the rapid visualization of analysis by output in GIF format.     

The analysis of Neisseria meningitidis proteomes: Reference maps and their applications

Neisseria meningitidis is an encapsulated Gram-negative bacterium responsible for significant morbidity and mortality worldwide. The availability of meningococcal genome sequences in combination with the rapid growth of proteomic techniques and other high-throughput methods, provided new approaches to the analysis of bacterial system biology. This review considers the meningococcal reference maps so far published as a starting point aimed to elucidate bacterial physiology and pathogenicity, paying particular attention to proteins with potential vaccine and diagnostic applications.     

Novel strategies to clone identical and distinct DNA sequences for several complex genomes

In this minireview I briefly describe the new methods suggested for cloning sequences identical by descent, homo-or hemizygously deleted, amplified or polymorphic, and compare them with the most efficient techniques developed earlier. The new methods include cloning of identical sequences (CIS), cloning of polymorphic sequences (COP), and cloning of deleted sequences (CODE). Although these methods are based on the same combination of biochemical techniques, their aims are different. These methods are fully complementary, and they may be combined to analyze a given object. If one aims to clone a disease gene responsible for familial cancer syndrome, these methods may be applied as follows. CIS can be used to identify the sequences identical by descent comparing the DNA obtained from affected or unaffected family members. COP can be used to find sequences that are different between affected and unaffected members, and CODE would be useful to compare tumor and normal (control) samples to isolate, deleted sequences (putative candidate tumor suppressor genes) and amplified sequences (putative oncogenes). The COP and CODE procedures can be applied to analyze the CpG islands, thus allowing direct candidate gene identification.