MacT: Apple Macintosh programs for constructing phylogenetic trees

MacT is a set of programs for the Apple Macintosh to constructand evaluate unrooted trees derived from amino acid sequencesusing a distance matrix method. Programs are designed on a ‘oneprogram–one task’ basis for (i) determining thebranching order in trees consisting of four or five speciesand calculating various statistical measures, (ii) calculatingstatistical measures for all possible topologies of unrootedtrees and (iii) generating and evaluating trees derived frombootstrapped samples. With four auxiliary programs unrootedtrees can be built for maximal 26 species, and the robustnessof topologies be tested by bootstrapping.     

Computer programs for nucleic acid sequence manipulation

Computer programs are described which help during the collection and analysis of nucleic acid sequence data. They are written in FORTRAN and have been implemented on a PDP 11/60 computer.     

MacPattern: protein pattern searching on the Apple Macintosh

A program is described for rapid detection of protein sequencepatterns on the Apple Macintosh which makes full use of theinformation contained in the PROSITE protein pattern database.     

An improved sequence handling package that runs on the Apple Macintosh

We report improvements to our sequence analysis package andadaptation to run on the Apple Macintosh range of machines.The ‘standard’ version of the programs, which runon a VAX, has been given a new user interface that makes theprograms very much easier to work with and has facilitated themove to the Macintosh. The reorganization of the code shouldsimplify moves to other systems that offer WIMP user interfaces.In addition to a large number of small but useful extra features,some important new analytical functions have been devised. Theseinclude sequence and contig editors; optimal alignment and comparisonmethods; and a new method for comparing the observed and expectedfrequencies of selected oligonucleotides. Received on February 12, 1990; accepted on April 19, 1990     

The DNA inspector II a program for analyzing and manipulating DNA sequence on the Apple Macintosh

This paper describes a new set of linked programs for analyzing and manipulating DNA sequences using the Apple Macintosh computer. The Macintosh is ideally suited for this purpose because of its extensive use of icons, pull-down menus, and dialog boxes, which form a very intuitive user interface, and its high-resolution graphics, which produce brilliant displays. Because of the extreme ease of use, the learning time for using the program is literally on the order of 5–10 minutes, thus making available computer analyses for many molecular geneticists who previously were not willing to invest the larger amount of time needed to learn how to run the analysis routines in other programs. The DNA Inspector II carries out all of the day-to-day routines needed in a molecular genetics lab. Results of the analyses can be saved to disk, printed, or transferred directly to other applications (e.g., word processing) through the “clipboard, ” an area of memory shared by all applications. The availability of Apple's relatively low-cost LaserWriter printer allows publication-quality figures to be generated very easily from within the program.     

MacP 12: a protein property multi-profile plot program for the Apple Macintosh

MacP12, a program for the Apple Macintosh, allows simultaneousplotting of two protein property profiles selectable from 12built-in amino acid property scales. Various parameters suchas the region to be analyzed, the size of the sliding window,the weighting function and the size of the graphical outputcan be easily adjusted by the user, which makes this programappropriate for diverse research questions. Since built-in scalescan be simply exchanged, MacP12 is adaptable to the specificneeds of the individual user.     

Macintosh sequence analysis software

The analysis of information in nucleotide and amino acid sequence data from an investigator’s own laboratory, or from the ever-growing worldwide databases, is critically dependent on well planned and written software. Although the most powerful packages previously have been confined to workstations, there has been a dramatic increase over the last few years in the sophistication of the programs available for personal computers, as the speed and power of these have increased. A wide choice of software is available for the Macintosh, including the LaserGene suite of programs from DNAStar. This review assesses the strengths and weaknesses of LaserGene and concludes that it provides a useful and comprehensive range of sequence analysis tools.     

Clustal W—蛋白质与核酸序列分析软件

蛋白质与核酸的序列分析在现代生物学和生物信息学中发挥着重要作用,新的算法和软件层出不穷,本文介绍一个可运行在ＰＣ机上的完全免费的多序列比较软件－ＣｌｕｓｔａｌＷ,它不但可以进行蛋白质与核酸的多序列比较,分析不同序列之间的相似性关系,还可以绘制进化树。由于其灵活的输入输出格式、方便的参数设定和选择、详尽的在线帮助以及良好的可移植性,使得ＣｌｕｓｔａｌＷ在蛋白质与核酸的序列分析中得到了广泛应用。     

A dual-tag microarray platform for high-performance nucleic acid and protein analyses

DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve specificity of detection and dynamic range. To further extend the utility of DNA microarray-based approaches we present a high-performance tag microarray procedure that enables probe-based analysis of as little as 100 target cDNA molecules, and with a linear dynamic range close to 10⁵. Furthermore, the protocol radically decreases the risk of cross-hybridization on microarrays compared to current approaches, and it also allows for quantification by single-molecule analysis and real-time on-chip monitoring of rolling-circle amplification. We provide proof of concept for microarray-based measurement of both mRNA molecules and of proteins, converted to tag DNA sequences by padlock and proximity probe ligation, respectively.     

Compression of nucleic acid and protein sequence data

This paper describes the application of text compression methodsto machine-readable files of nucleic acid and protein sequencedata. Two main methods are used to reduce the storage requirementsof such files, these being n-gram coding and run-length coding.A Pascal program combining both of these techniques resultedin a compression figure of 74.6% for the GenBank database anda program that used only n-gram coding gave a compression figureof 42.8% for the Protein Identification Resource database. Received on November 29, 1985; accepted on February 24, 1986     

MBIS--an integrated system for the retrieval and analyses of sequence data from nucleic acids and proteins.

A computer-based system termed MBIS (the Molecular Biological Information Service), written in FORTRAN77 and Digital Command Language (DCL) and running on a Digital Equipment Corporation VAX computer under the VMS operating system (V4.1) is in use at the Division of Molecular Biology. MBIS consists of three main sections: 1) The utility section, used by the system's manager to tailor the five commonly available databases so that they are useable by the applications programmes running on the system; 2) The retrieval section, used to find and extract specific sequences or bibliographic information, and 3) The analytical section, used to analyse and compare sequences either extracted from the databases or input by the user. The nucleotide databases maintained are GenBank, EMBL and PIR (Protein Identification Resource, National Biomedical Research Foundation) and the peptide databases are PIR and NEWAT. In addition, users can originate and maintain their own databases. Those programmes which feature graphics output are compatible with most emulators of the Tektronix 4010 terminal.     

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

Background  

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data.     

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     

'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers

DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.     

Non-parametric statistics for nucleic acid sequence study

The use of non-parametric statistics for nucleic acid sequence studies is illustrated by some examples. This method is highly flexible and allows design of specific tests for detecting sequence structure. Tests devoted to local repetitivity, codon nearest neighbors, and dinucleotide avoidance are discussed in detail. An appendix indicates all computations required to use these tests.     

A Macintosh program for the versatile generation of random nucleic acid sequences and their structural analysis

The program ‘MacStAn’ for the Apple Macintosh generatesrandom sequences and can analyze their tendency to form secondarystructure or translation products as well as their mono-, di-and trinucleotide composition. Generation of random sequencesis versatile in that one can (i) predefine the G + C content,maximal base repetitions and constant regions; (ii) preset theentire dinucleotide composition; or (iii) shuffle an existingsequence. The program constitutes an integrated package witha graphical user interface, fill-featured editing, saving, printing,text import and export, dot plot and sequence alignment.