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.     

Software Tools for DNA Sequence Design

The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.     

An improved algorithm for nucleic acid secondary structure display

An improved algorithm for the display of nucleic acid secondary structures is presented. It is particularly suitable for large sequence segments and it automatically generates an aesthetically pleasing display of the structure with very limited overlap of strands. Structural similarities in different structures are conserved in the display thus greatly aiding structural homology comparisons. Using the algorithm, we illustrate the effect of ribosome translocation on the secondary structure of a rat neuropeptide messenger RNA.     

Developing an erection scheme for a large bridge

In the erection of large bridges the structure is successively analysed at each critical stage in the sequence. Invariably such structures are erected by first building the primary structural members, either by cantilevering them forward or lifting them into position, and following this by adding such secondary members as cantilevers, cross members and concrete slabs. The effect of these secondary members is to change the structural characteristics of the bridge and consequently the analysis must be able to take account of this history throughout the sequence.The LEAP suite of programs has been used on several major bridges to analyse and develop viable erection schemes and, using FRIDAY, to assess the critical stages and identify the most highly stressed members.This paper describes in a general way the methods used, and shows examples of the procedure for the particular case of the large cable-stayed West Gate Bridge in Australia.     

A set of Macintosh computer programs for the design and analysis of synthetic genes

Computer programs that can be used for the design of synthetic genes and that are run on an Apple Macintosh computer are described. These programs determine nucleic acid sequences encoding amino acid sequences. They select DNA sequences based on codon usage as specified by the user, and determine the placement of base changes that can be used to create restriction enzyme sites without altering the amino acid sequence. A new algorithm for finding restriction sites by translating the restriction endonuclease target sequence in all three reading frames and then searching the given peptide or protein amino acid sequence with these short restriction enzyme peptide sequences is described. Examples are given for the creation of synthetic DNA sequences for the bovine prethrombin-2 and ribonuclease A genes.     

A secondary and tertiary structure editor for nucleic acids

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.     

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.     

Two-dimensional abstract representations (signatures) of proteins

Algorithms have been developed to allow two-dimensional abstract representations of proteins based on: (i) a non-redundant subset of codons, (ii) hydropathy values of amino acids, (iii) the polarities of the amino acid residues and (iv) predicted secondary structures. In addition the suggestion of Gates on nucleic acid representation was implemented. The two-dimensional projections (signatures) that are obtained have the merit that several plots can be represented simultaneously for ready visualization. The approach appears useful in showing relationships among groups of proteins.     

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.     

EMBLSCAN: fast approximate DNA database searches on compact disc.

An algorithm that allows rapid searching of nucleic acid sequences based on pregenerated index files is described. The programs and index files for searching the entire EMBL nucleotide sequence collection are being distributed on the EMBL Data Library's CD-ROM.     

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.     

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。     

IBM microcomputer programs that analyze DNA sequences for tRNA genes

A set of four computer programs that search DNA sequence data files for transfer RNA genes have been written in IBM (Microsoft) BASIC for the IBM personal computer. These programs locate and plot predicted secondary structures of tRNA genes in the cloverleaf conformation. The set of programs are applicable to eukaryotic tRNA genes, including those containing intervening sequences, and to prokaryotic and mitochondrial tRNA genes. In addition, two of the programs search up to 150 residues downstream of tRNA gene sequences for possible eukaryotic RNA polymerase III termination sites comprised of at least four consecutive T residues. Molecular biologists studying a variety of gene sequence and flanking regions can use these programs to search for the additional presence of tRNA genes. Furthermore, investigators studying tRNA gene structure-to-function relationships would not need to do extensive restriction mapping to locate tRNA gene sequences within their cloned DNA fragments.     

An extension of the graph theoretical approach to predict the secondary structure of large RNAs: the complex of 16S and 23S rRNAs from E. coli as a case study

An algorithm using the graph theoretical approach to predict secondary structures of large nucleic acids is discussed. Reliability of prediction can be improved by incorporating available experimental data and sequence homology information. As a case study, this algorithm is applied to predict the secondary structure of the 16S-23S rRNA complex from E. coli. It was found that several structures of the complex can coexist. The computer program developed to predict the secondary structure of large RNAs can be run on IBM PC/AT compatible systems.     

An Efficient 2½ D rendering and Compositing System

We describe a method for doing image compositing using either 2D geometric shapes or raster images as input primitives. The resolution of the final image is virtually unlimited but, as no frame buffer is used, performance is much less dependant on resolution than with standard painting programs, allowing rendering very large images in reasonable time. Many standard features found in compositing programs have been implemented, like hierarchical data structures for input primitives, lighting control for each layer and filter operations (for antialiasing or defocus).     

Task-oriented programming of large redundant robot motion

Large robots are a new domain of advanced robotics. Examples of their application fields are tasks like operations on large free-form surfaces, especially aircraft cleaning and removing paint from hulls. They are equipped with a programmable robot control comparable to a control system used for industrial robots. However, conventional teach-in methods are not able to manage the complexity of programming large redundant robot operation on free-form geometries. The Fraunhofer IPA has developed an innovative off-line programming system that allows the creation of robot motion programs which satisfy time and energy optimization criteria. This system helps to avoid collisions within the workspace and to fulfill conditions that arise from the robot kinematics and dynamics. This advanced programming system has been successfully used to generate motion programs for the world's largest mobile robot, the aircraft cleaning manipulator SKYWASH. In this context offline programs for eleven different types of aircraft have been developed.     

Inferring consensus structure from nucleic acid sequences

This paper presents an unsupervised inference method for determining the higher-order structure from sequence data. The method is general, but in this paper it is applied to nucleic acid sequences in determining the secondary (2-D) and tertiary (3-D) structure of the macromolecule. The method evaluates position - position interdependence of the sequence using an information measure known as expected mutual information. The expected mutual information is calculated for each pair of positions and the chi-square test is used to screen statistically significant position pairs. In the calculation of expected mutual information, an unbiased probability estimator is used to overcome the problem associated with zero observation in conserved sites. A selection criterion based on known structural constraints of the strongest interdependent position pairs is applied yielding position pairs most indicative of secondary and tertiary interactions. The method has been tested using tRNA and 5S rRNA sequences with very good results.     

Automatic detection of conserved base pairing patterns in RNA virus genomes.

Almost all RNA molecules--and consequently also almost all subsequences of a large RNA molecule-form secondary structures. The presence of secondary structure in itself therefore does not indicate any functional significance. In fact, we cannot expect a conserved secondary structure for all parts of a viral genome or a mRNA, even if there is a significant level of sequence conservation. We present a novel method for detecting conserved RNA secondary structures in a family of related RNA sequences. The method is based on combining the prediction of base pair probability matrices and comparative sequence analysis. It can be applied to small sets of long sequences and does not require a prior knowledge of conserved sequence or structure motifs. As such it can be used to scan large amounts of sequence data for regions that warrant further experimental investigation. Applications to complete genomic RNAs of some viruses show that in all cases the known secondary structure features are identified. In addition, we predict a substantial number of conserved structural elements which have not been described so far.