基于代理程序开发核酸序列二次数据库

以构建核酸序列二次数据库为目的,基于Windows操作系统下,编译Web代理程序,介绍开发核酸序列二次数据库的一般过程。研究通用代理程序开发本地化核酸序列二次数据库的具体步骤,所涉及的关键技术以及常见问题解决。解决了生物信息数据繁多与数据处理工作量大问题,经反复调试基本实现了示例程序核酸序列二级数据库系统的构建。     

PRONUC: a software package for the analysis of protein and nucleic acid sequences

PRONUC is a menu-driven software package from which a molecular biologist may gain access to a variety of tools for the analysis of protein and nucleic acid sequences. Features include various algorithms for sequence comparisons, secondary structure prediction, sequence manipulation (translation complementation etc.) and finding restriction enzyme cut-sites. The sequences under study can be retrieved from several databases of published sequences or a users sequence(s) can be entered by means of a sequence editor or retrieved from a database constructed by the user. PRONUC comes with a comprehensive manual and on-line help which reflects several years of user feedback and is available for Digital VAX computer systems running the VMS or micro-VMS operating system.     

ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage

ACNUC is a database structure and retrieval software for use with either the GenBank or EMBL nucleic acid sequence data collections. The nucleotide and textual data furnished by both collections are each restructured into a database that allows sequence retrieval on a multi-criterion basis. The main selection criteria are: species (or higher order taxon), keyword, reference, journal, author, and organelle; all logical combinations of these criteria can be used. Direct access to sequence regions that code for a specific product (protein, tRNA or rRNA) is provided. A versatile extraction procedure copies selected sequences, or fragments of them, from the database to user files suitable to be analysed by user-supplied application programs. A detailed help mechanism is provided to aid the user at any time during the retrieval session. All software has been written in FORTRAN 77 which guarantees a high degree of transportability to minicomputers or mainframes.     

Visualization of nucleic acid sequence structural information

Several interactive Pascal programs have been written for the analysis and display of structural information in nucleic acid sequences. Layout procedures were developed to display the homology and repeat matrices of a sequence and to predict and display the secondary structure of RNA/DNA molecules free of overlap and to predict and display internal repeats. No special plotting devices are required because the output is adapted to line printers. Sequences from several DNA database systems can be used as input. These programs are part of a general nucleic acid sequence analysis package.     

Automatic evaluation of protein sequence functional patterns

A procedure that automatically provides an evaluation of the diagnostic ability of a protein sequence functional pattern is described. The procedure relies on the identification of the closest definable set in terms of a (protein sequence) database functional annotation to the set of database instances containing a given pattern. Assuming annotation correctness and completeness in the protein sequence database, the degree of statistical association between these sets provides an appropriate measure of the diagnostic ability of the pattern. An experimental implementation of the procedure, using the NBRF/PIR protein database, has been applied to a diverse collection of published sequence patterns. Results obtained reveal that frequently it is not possible to define (in NBRF/PIR database terminology) the set of database instances containing a given pattern, suggesting either lack of pattern diagnostic ability or protein database annotation incompleteness and/or inconsistencies.     

A mechanism for maintaining an up-to-date GenBank database via Usenet

In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems.     

Particle Swarm Optimisation for Protein Motif Discovery

In this paper, a modified particle swarm optimisation algorithm is proposed for protein sequence motif discovery. Protein sequences are represented as a chain of symbols and a protein sequence motif is a short sequence that exists in most of the protein sequence families. Protein sequence symbols are converted into numbers using a one to one amino acid translation table. The simulation uses EGF protein and C2H2 Zinc Finger protein families obtained from the PROSITE database. Simulation results show that the modified particle swarm optimisation algorithm is effective in obtaining global optimum sequence patterns, achieving 96.9 and 99.5 classification accuracy respectively in EGF and C2H2 Zinc Finger protein families. A better true positive hit result is achieved when compared to the motifs published in PROSITE database.     

Classification neural networks for rapid sequence annotation and automated database organization

A neural network classification method has been developed as an alternative approach to the search/organization problem of large molecular databases. Two artificial neural systems have been implemented on a Cray for rapid protein/nucleic acid classification of unknown sequences. The system employs a n-gram hashing function for sequence encoding and modular back-propagation networks for classification. The protein system, which classifies proteins into PIR (Protein Identification Resource) superfamilies, has achieved 82–100% sensitivity at a speed that is about an order of magnitude faster than other search methods. The pilot nucleic acid system showed a 91–97% classification accuracy. The software tool could be used as a filter program to reduce the database search time and help organize the molecular sequence databases. The tool is generally applicable to any databases that are organized according to family relationships.     

多媒体数据库索引技术的研究与实现

现有的数据库索引技术,普遍不能适应多维空间属性的搜索,特别是无法对大容量的多媒体数据进行基于内容的检索。文章分析研究了多媒体数据库的索引结构和索引算法,设计了一种用于大容量图像数据库的索引方法。实验在1万多幅的图像库上反复进行,结论证明该算法能够有效地支持大容量图像库的基于内容检索。     

基于事务序列的视频摘要挖掘方法研究

提出了一种基于事务序列的关联挖掘方法实现对足球视频的摘要挖掘。处理过程分为视频数据预处理、视频属性提取和视频摘要挖掘等三个步骤。视频数据预处理阶段将原始视频流切分成物理镜头。视频属性提取阶段先将物理镜头分成五种类型,将视频转换成镜头标识序列,以事务为单位对标识序列进行切分形成事务序列,构造一种关系数据库来存储这些事物序列数据。在视频摘要挖掘阶段,采用传统的Apriori算法对事务数据库进行关联挖掘获得关联模式,以挖掘出的关联模式为依据形成视频摘要。实验结果表明,挖掘精彩事件的查全率和查准率较高,具有实用价值。     

Compression of nucleic acid and protein sequence data

This paper describes the application of text compression methods to machine-readable files of nucleic acid and protein sequence data. Two main methods are used to reduce the storage requirements of such files, these being n-gram coding and run-length coding. A Pascal program combining both of these techniques resulted in a compression figure of 74.6% for the GenBank data-base and a program that used only n-gram coding gave a compression figure of 42.8% for the Protein Identification Resource database.     

Easy to use and rapid isolation and detection of a viral nucleic acid by using paramagnetic microparticles and carbon nanotubes-based screen-printed electrodes

A method that is easy to use, rapid, with a low cost of detecting viral nucleic acid in a biological sample represents the essential tool in targeted therapy. In this study, we report the use of paramagnetic microparticles covered by streptavidin and modified by an oligonucleotide probe with a specific viral sequence labeled by biotin to detect human immunodeficiency virus (HIV) and influenza virus subtype H5N1. The viral nucleic acids were primarily detected by adsorptive transfer stripping technique coupled with square wave voltammetry using carbon paste, hanging mercury drop or carbon nanotubes-based screen-printed working electrodes. Detection limits were estimated for both sequences down to picograms per 3 μl. To isolate the viral sequences, paramagnetic microparticles covered with biotin-labeled oligonucleotides were used. We calculated the yield of isolation for H5N1 and/or HIV sequences, which was defined as “isolated concentration of viral nucleic acid sequence”/“given viral nucleic acid sequence” × 100. We estimated the yield for both sequences as 59%. Moreover, we studied the influence of human serum, dsDNA and non-complementary sequence of nucleic acids on isolation of viral nucleic acids. We also used carbon nanotubes-based screen-printed electrodes coupled with micro-flow instrument to detect viral nucleic acids. We were able to isolate and detect nanogram amounts of nucleic acids.     

CORGEN: a FORTRAN-77 generator of standard and non-standard DNA helices from the sequence

An analytical procedure CORGEN generates a variety of DNA double-stranded structures from user-supplied sequence using a nucleic acid database incorporated into a standard FORTRAN-77 program. Alternatively, the cylindrical polar coordinates of DNA components may be supplied from the external table. An algorithm that performs intercalation sites in DNA is described. This procedure can be used to generate complexes of antibiotics with DNA. Non-standard DNA structures can be built by alternating the global helical twist and global helical rise in the regular DNA helix. The procedures described can be used for computer generation of a variety of non-standard DNA structures which can be subjected to molecular mechanics and dynamics simulations.     

Study of protein sequence comparison metrics on the connection machine CM-2

Software tools have been developed to do rapid, large-scale protein sequence comparisons on databases of amino acid sequences, using a data parallel computer architecture. This software enables one to compare a protein against a database of several thousand proteins in the same time required by a conventional computer to do a single protein-protein comparison, thus enabling biologists to find relevant similarities much more quickly, and to evaluate many different comparison metrics in a reasonable period of time. We have used this software to analyze the effectiveness of various scoring metrics in determining sequence similarity, and to generate statistical information about the behavior of these scoring systems under the variation of certain parameters.An earlier version of this paper was presented at Supercomputing '88.Eric Lander was supported in part by National Science Foundation grant #NSF-DCB-8611317 and System Development Foundation grant #SDF612     

Hypercard-based data management tools for molecular biologists.

I have designed a Macintosh data management system for molecular biologists. This system, called DataMinder, can be used to store information about oligonucleotides, nucleic acid or protein sequences, recombinant DNA clones, cells, reagents and protocols. DataMinder is not limited to data storage. A number of utilities for data analysis are provided, including those for the evaluation of oligonucleotides for use as hybridization probes or primers for DNA synthesis, and a variety of sequence editing features. Context-sensitive help is available on-line. DataMinder is simple to use and to customize and allows for sharing of database information across a computer network.     

对步态空时数据的连续特征子空间分析

提出一种基于空时特征提取的人体步态识别算法。连续的特征子空间学习依次提取出步态的时间与空间特征：第一次特征子空间学习对步态的频域数据进行主成分分析,步态数据被转化为周期特征矢量;第二次特征子空间学习对步态数据的周期特征矢量形式进行主成分分析加线性判别分析的联合分析,步态数据被进一步转化为步态特征矢量。步态特征矢量同时包含运动的周期特征以及人体的形态特征,具有很强的识别能力。在USF步态数据库上的实验结果显示,该算法识别率较其他同类算法有明显提升。     

Automatic updating of the EMBL database via EMBNet

The paper describes a procedure for updating the EMBL (European Molecular Biology Laboratory, Heidelberg) database of nucleic acid sequences and its indexes used by the University of Wisconsin Genetics Computer Group (GCG) software package, using updated entries for this database distributed via EMBNet. At present the procedure is being run on a MRC Clinical Research Centre's (CRC) SUN 4/280 server using SUNOS version 4.0.1 operating system.     

Six Ways from Sunday: Approaches to Indexing Digital Text Images

In 1994, the Andrew W. Mellon Foundation funded a joint project undertaken by the Center for Research Libraries (CRL) and the Latin American Microfilm Project (LAMP) to scan and index over three-hundred thousand pages of microfilmed Brazilian Government Documents for the Internet. Due to the collection size, format, language and poor physical condition of the text, entering this overwhelmingly textual collection as full-text was prohibitively expensive. Instead the documents were scanned as images, thereby maintaining the intellectual content of the collection, but losing the dynamic searching capabilities inherent in full-text databases. A combination of indexing approaches was used to provide access to these documents. Indexing (table-of-contents, pagination and subject indexes) found in the documents were recreated to give users access to the documents. A controlled vocabulary was established to index a portion of the database. The factors of costs, user feedback and available technologies all influenced the choices of the five indexes ultimately utilized. This paper will describe and comment on the strengths and weaknesses of the various indexing approaches taken to access the images within this database.     

基于多级Gabor变换序列特征的人脸识别

鉴于Gabor特征对光照、表情等变化具有鲁棒性,在寻找局部细节特征和全局轮廓特征的描述方面,提出一种基于多级局部多通道Gabor变换序列特征的人脸描述与识别方法。对人脸图像进行多级分块和对局部子块进行多方向、多分辨率Gabor小波滤波,并提取其对应不同方向、不同尺度的多个Gabor幅值域图谱(LGMM),将各级子图像的图谱LGMM进行连接后形成多级Gabor幅值域图谱,使用径向基网络对特征进行识别。对人脸库ORL和YEL的识别实验进行对比,结果验证了该方法的有效性。