Useful Microsoft Word Macros for molecular biologists and protein chemists

Biologists today make extensive use of word processing programs for the production of research reports, literature reviews and grant proposals. Frequently, such programs become the default platform for viewing and the later publication of protein and nucleic acid sequence data. Thus, researchers often switch between their word processor and more specialized programs designed to analyze protein and nucleic acid sequences. It would be more convenient to perform these simple sequence analyses using the word processor without switching to another program. The focus here is on the use of the Visual Basic programming language, which is built into all recent versions of Microsoft Word to generate surprisingly complex and useful macros that can conveniently analyze several important features of protein and nucleic acid sequences. The standard Word interface can also be easily modified to display and run these macros from a pull-down menu. Several examples of this approach are provided.     

Screening protein and nucleic acid sequences against libraries of patterns.

We describe programs that can screen nucleic acid and protein sequences against libraries of motifs and patterns. Such comparisons are likely to play an important role in interpreting the function of sequences determined during large scale sequencing projects. In addition we report programs for converting the Prosite protein motif library into a form that is compatible with our searching programs. The programs work on VAX and SUN computers.     

A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

A computer package written in Fortran-IV for the PDP-11 minicomputer is described. The package's novel features are: software for voice-entry of sequence data; a less memory intensive algorithm for optimal sequence alignment; and programs that fit statistical models to nucleic acid and protein sequences.     

Computer programs for the analysis of nucleotide sequences (MALK)

A system for the computer analysis of nucleic acid and protein sequences ("Helix") is described. Format of the DNA sequences is EMBL--compatible and may be easily commented with the help of convenient menus. "Helix" has also following possibilities: an effective alignment of gele reading data and formation of the final sequence; simple making of recombined molecules "in calcular"; calculations of nucleotide and dinucleotide distribution along the sequence; looking for coding frames; calculations percentage of codons and amino acids in coding frames; searching for direct and inverted repeats; sequences alignment; protein secondary structure prediction; restriction mapping; DNA--protein translation. "Helix" also contain programs for RNA-structure prediction, looking for homologies throughover the EMAL bank, choosing optimal sequence for probes and searching promoters. All the programs are written at FORTRAN-77 and automatically translated into FORTRAN-4. "Helix" require only 64 kbite.     

Apple Macintosh programs for nucleic and protein sequence analyses

This paper describes a package of programs for handling and analyzing nucleic acid and protein sequences using the Apple Macintosh microcomputer. There are three important features of these programs: first, because of the now classical Macintosh interface the programs can be easily used by persons with little or no computer experience. Second, it is possible to save all the data, written in an editable scrolling text window or drawn in a graphic window, as files that can be directly used either as word processing documents or as picture documents. Third, sequences can be easily exchanged with any other computer. The package is composed of thirteen programs, written in Pascal programming language.     

Interactive computer programs in sequence data analysis

We present interactive computer programs for the analysis of nucleic acid sequences. In order to handle these programs, minimum computer experience is sufficient. The nucleotide sequence of the human gamma globin gene complex is used as an example to illustrate the data analysis.     

Protein structural models for nucleic acid interactions

It is proposed that particular segments of some ribosomal, histone and plant viral capsid proteins adopt a helical structural mode for interaction with nucleic acid. The amino acid regions were determined by three probes applied to 26 protein sequences: searches for helical wheels displaying asymmetric basic charge distributions, secondary structural predictions, and searches for primary structural homologies. In 11 of the protein sequences examined, homologous heptapeptides were found in the residue spans delineated by the three probes. A helical wheel analysis of the oligopeptide amino acids showed a distinct positive charge clustering. It is suggested that the basic amino acid side chains on the hydrophilic helical side interact with nucleic acid negative phosphate groups while the somewhat hydrophobic side is available for interaction within the protein or possibly with the major groove of double-stranded nucleic acid.     

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

Computer programs that can be used for the design of syntheticgenes and that are run on an Apple Macintosh computer are described.These programs determine nucleic acid sequences encoding aminoacid sequences. They select DNA sequences based on codon usageas specified by the user, and determine the placement of basechanges that can be used to create restriction enzyme siteswithout altering the amino acid sequence. A new algorithm forfinding restriction sites by translating the restriction endonucleasetarget sequence in all three reading frames and then searchingthe given peptide or protein amino acid sequence with theseshort restriction enzyme peptide sequences is described. Examplesare given for the creation of synthetic DNA sequences for thebovine prethrombin-2 and ribonuclease A genes Received on October 18, 1988; accepted on December 9, 1988     

猪胸膜肺炎放线杆菌转铁结合蛋白基因（rbp8）分析及建模

为了深入研究猪胸膜肺炎放线杆菌（Actinobacillus pleuropneumonie,App）转铁结合蛋白基因（Transferrin BindingProtein8,脚）的生物学特性,采用生物信息学方法,对GenBank中的5株App的TbpB的核酸及其氨基酸序列进行比对,选取其中的中国湖北分离株（JL03）对其分子结构、理化性质及功能域、蛋白质二级和三级结构等重要参数进行了预测和分析,并在三级结构的基础上进行了同源建模。结果表明,不同APP菌株之间核酸序列相似性较大,而氨基酸序列存在较大差异,二级结构以延伸链和随机卷曲为主要构件,其空间结构与脑膜炎双球菌GNAl870蛋白相似性较高,以此为模板成功构建了三维结构分子模型,为TbpB基因功能的深入研究提供了线索和参考依据。     

The design of synthetic genes

Computer programs are described that aid in the design of synthetic genes coding for proteins that are targets of a research program in site directed mutagenesis. These programs "reverse-translate" protein sequences into general nucleic acid sequences (those where codons have not yet been selected), map restriction sites into general DNA sequences, identify points in the synthetic gene where unique restriction sites can be introduced, and assist in the design of genes coding for hybrids and evolutionary intermediates between homologous proteins. Application of these programs therefore facilitates the use of modular mutagenesis to create variants of proteins, and the implementation of evolutionary guidance as a strategy for selecting mutants.     

Los Alamos sequence analysis package for nucleic acids and proteins.

An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a large-scale database can be used for comparative studies on sequence and structural homologies in order to find unnoted information stored in nucleic acid sequences.     

Multiple sequence alignment with the Clustal series of programs

The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).     

Sequence search on a supercomputer.

A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.     

在AppleⅡ型微机上实现核酸数据处理的工作程序

本文报道了在AppleⅡ型微机上实现核酸数据处理的一系列工作程序。应用这些程序,可进行核酸数据的贮存、对指定的核酸数据结构的改造、限制性内切酶识别位点的检索、核酸序列至蛋白序列的翻译、相关核酸序列及蛋白序列的同源性比较、氨基酸密码使用频率的统计和基因的启动子结构的初步探索等方面的工作。     

A convenient and adaptable microcomputer environment for DNA and protein sequence manipulation and analysis.

We describe the further development of a widely used package of DNA and protein sequence analysis programs for microcomputers (1,2,3). The package now provides a screen oriented user interface, and an enhanced working environment with powerful formatting, disk access, and memory management tools. The new GenBank floppy disk database is supported transparently to the user and a similar version of the NBRF protein database is provided. The programs can use sequence file annotation to automatically annotate printouts and translate or extract specified regions from sequences by name. The sequence comparison programs can now perform a 5000 X 5000 bp analysis in 12 minutes on an IBM PC. A program to locate potential protein coding regions in nucleic acids, a digitizer interface, and other additions are also described.     

mRNA sequence predictions from homologous protein sequences

A model has been developed that permits the prediction of mRNA nucleic acid sequence from the sequences of the translated proteins. The model relies on the information obtained from the comparison of protein sequences in related species to reduce the number of possible codons for those amino acids where mutations are observed. The predictions so obtained have been tested by applying the model to proteins whose mRNA sequences are known. The model's predictions have been found to be 100% accurate if three or more different amino acids are known at a given position and if the protein sequences are restricted to relatively closely related species (within the same class). The use of this model may permit a reduction of the mRNA sequence degeneracy and therefore be helpful in the synthesis of cDNA probes or for the prediction of restriction endonuclease sites. Computer programs have been developed to ease the use of the model.     

WebVar: A resource for the rapid estimation of relative site variability from multiple sequence alignments

WebVar is an online resource that provides estimates of relative site variability from multiple alignments of homologous protein or nucleic acid sequences. WebVar provides a variety of graphic and textual representations of estimates, designed to assist in phylogenetic analysis. AVAILABILITY: The WebVar server is located at http://www.pesolelab.it/Tools/WebVar.html     

核酸顺序的计算机辅助分析系统

本文介绍了一个在微机(IBM PC)上实现的、用于核酸顺序分析的计算机程序系统.该系统由三个层次和18个功能块构成,菜单及人机对话使得用户能较快地掌握和使用它.在编程中,采用了树结构、先进后出栈和稀疏矩阵等数据结构技巧,运用了Bayes法等统计分析方法,Kruskal算法和Floyd算法等一系列图论方法也被得到应用,这个软件系统的推出对于分子生物学研究具有一定的积极作用.     

A sense of closeness: protein detection by proximity ligation

Highly specific and sensitive procedures will be required to evaluate proteomes. Proximity ligation is a recently introduced mechanism for protein analysis. In this technique, the convergence of sets of protein-binding reagents on individual target molecules juxtaposes attached nucleic acid sequences. Through a ligation reaction a DNA reporter sequence is created, which can be amplified. The procedure thus encodes detected proteins as specific nucleic acid sequences in what may be viewed as a reverse translation reaction.