A computer program for translating DNA sequences into protein.

This paper describes a comprehensive program for translating one or two DNA sequences into amino acid sequences. Written in FORTRAN, it was designed for maximum flexibility of use and easy maintenance, modification and portability. It has full comments throughout.     

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given.     

MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences

This paper presents a method for the multiple alignment of asequence set. The MASH algorithm uses a non-redundant databaseof common motifs and an ‘alignment priority’ criterionthat depends on the length and the occurrence frequency of thepatterns in the set of sequences. This user-defined criterionallows the determination of the series of the patterns to bealigned. This program is applied to a fragment of envelope geneenv gp120 for 20 isolates of the immunodeficiency virus. Themultiplicity of alignments obtained by modifying the criterionparameters reveals different aspects of similarity between thesequences. Received on June 4, 1990; accepted on December 14, 1990     

The STRESS program: A computer program for the analysis of stresses in long bones

A computer program was developed to compute torsional and bending stresses in long bones. The input format for the program is designed to be as convenient to the user as possible, allowing him to transmit to the program only as many points as he feels are required to describe the cross-sectional geometry. The program permits the user to specify by which method torsional stresses are to be computed, what type of stresses are to be computed, and to what accuracy the results are desired. Computation times are of the order of 5 sec or less (on an IBM 360), making use of the program more economical than manual computations.     

A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.     

The assessment of patient prognosis using an interactive computer program

The use of chronic disease probabilistic models to calculate patient prognosis is presented. The method relies on the calculation of transition probabilities between discrete disease states from a patient data bank. Maximum likelihood estimates are used for each age and unwanted fluctuations are removed by a moving average. An interactive computer program was written and the method applied to the calculation of the probability of stroke and myocardial infarction for male patients on antihypertensive therapy. A clinician could obtain the prognostic information for a patient in less than one minute. Applications in medical student education are also discussed.     

Experiences with an interactive computer program for recording biometrical health screening data

The nurses measurements of biometrical health screening data comprise the central elements in our multiphasic preventitive medical investigation in Malmö. It is also vitally importantfor the formation processing, evaluation and actions of the screening that all test values and other data can be supplied to a uniform computer bank without delay in terms of secondary transferral routines. In our ongoing population investigation project in Malmö, this has been accomplished by on-line computer-programs for the different components of the screening. Here we describe the practical experiences with the subroutine used by the nurses to feed the biometrical test results to the computer bank.     

A computer program for comparative analysis of nucleic acid sequences.

The programs offer the possibility of comparing pairs of homologous sequences in order to find out percentage of homology, number of identical and deviating nucleotides, of transitions and transversions and, derived from these, KNUC-values according to Kimura (1) and the corresponding standard error sigmaK. The sequences can be printed in pairs underneath each other, homologies are indicated by asterisks between the identical nucleotides. Out of a set of homologous sequences stored on a disk any number of sequences can be compared in pairs in this way, and a matrix containing either the percentage of homology values, the number of deviating nucleotides or the KNUC-values together with the corresponding standard errors can be sent to screen, printer or disk. A program will be available soon which creates a dendrogram representing the similarity between the sequences by use of an average linkage clustering method deduced from this matrix. The programs are written for Apple II computers using UCSD-PASCAL and for Sirius I/Victor 9000 computers using TURBO-PASCAL.     

An interactive modeling program for DNA

An interactive program for modeling A-, B- and Z-DNA in a schematic and nonatomic representation has been developed for the Evans and Sutherland PS300. The program lets users display several molecules for which parameters determining the three-dimensional structure can be calculated either on the basis of theoretical models or inferred from experimental data. The calculation of the curvature and torsion of the helical axis, by a method based on Frenet's equations, makes it possible to quantify the effects of the parameters on the helical axis.     

A teaching exercise for the identification of bacteria using an interactive computer program

An interactive computer program written in Fortran is described which provides an exercise in the identification of bacteria. The program, IDEN, provides a novel way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. An unknown bacterium is assigned to a student who is provided with a list of possible species and a list of tests which may be carried out. The student's objective is the correct identification of the unknown in the most economical manner. An indication is given concerning the way in which this program can be used to enhance theoretical instruction and practical investigation.     

DNA Modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer

DNA Modeller is a microcomputer program for interactively manipulatingup to 20 bp in a DNA double helical arrangement. It calculatesthe van der Waals and electrostatic energies of base-base interactionsusing the AMBER potential, minimizes the energy with respectto the pair (buckle, propeller, opening, shear, stretch, stagger)and step (tilt, roll, twist, shift, slide, rise) parameters,calculates lengths of the canonical hydrogen bonds between thecomplementary bases, and calculates interatomic distances betweenthe successive base pairs. Input/output files are simple listsof the step and pair parameters or lists of the atom specifications(N1, C2, etc.) and their Cartesian coordinates (compatible withthe Desktop Molecular Modeller ^*.mol files). The program issupplied with a readbrk utility which transforms PDB/NDB tothe^*.mol format readable by DNA Modeller. The DNA crystal structuresdeposited in the PDB or NDB databases can thus be analyzed,and their bases visualized and interactively manipulated. Inaddition, DNA Modeller can calculate the base pair and stepgeometrical parameters and interaction energies. A plotter utilitycreates wire mono or stereo pictures of the bases. This programis designed for IBM-compatible computers working under DOS orcan run as a DOS application under MS Windows 3.x or Merge (SCOUnix DOS emulator).     

A Macintosh computer program for designing DNA sequences that code for specific peptides and proteins

A computer program (PINCERS) is described for use in the design of synthetic genes and mixed-probe DNA sequences. A protein sequence is reverse translated with generation of synonymous codons at each position producing a degenerate sequence. In order to locate potential restriction enzyme sites, the degenerate sequence is searched with a library of restriction enzymes for sites that utilize any combination of synonymous codons. These sites are indicated in a map so that they may be incorporated into the synthetic gene sequence. The program allows the user to select the appropriate codon usage table for the organism of interest and then to set a threshold usage frequency below which codons are not generated. PINCERS may also be used to assist in planning the synthesis of mixed-probe DNA sequences for cross-hybridization experiments. It can identify regions of specified length with the protein sequence that have the least overall degeneracy, thereby minimizing the number of probes to be synthesized and, therefore, maximizing the concentration of a given probe sequence.     

HYLAS: program for generating H curves (abstract three-dimensional representations of long DNA sequences)

The computer program HYLAS generates from a standard DNA lettersequence a three-dimensional space curve (H curve) which embodiesthe entire information content of the original nucleotide sequence.The program can display H curves either as two-dimensional (frontand side view) projections or as stereo-pair images. The curvescan be marked at specific nucleotide locations, annotated, rotatedfor observation from any viewing angle, and manipulated forconvenient side-by-side comparisons. Unlike the cumbersome lettersequences, H curves can be drastically condensed in size withoutlosing their ability to reflect the global nucleotide-distributionpattern of the entire DNA sequence. Often, biologically importantloci can be visually identified on the H curves. HYLAS is writtenin FORTRAN with separate mainframe (IBM- VM/CMS) and microcomputer(MS-DOS) versions. It uses the Tektronix-TCS library of graphicsubroutines. Received on October 24, 1988; accepted on July 15, 1989     

A dotplot program for the Atari ST, for the analysis of DNA and protein sequences

A program was written in GFA-BASIC for the Atari ST microcomputeraimed at drawing two-dimensional homology ‘dotplot’patterns for two protein or DNA sequences. The program, builtaround a machine-code subroutine, communicates interactivelywith the user by means of a multi-button dialogue panel andmouse-directed input. A 1000 x 1000 sequence comparison witha 14: 21 stringency window takes 12 s.     

BIOSITE: a program for the interactive comparison of aligned homologous protein sequences

A program, BIOSITE, providing for the interactive visual comparisonof aligned homologous amino-acid sequences is presented, includingan example of its application. The program allows for two typesof comparison sequence to be generated: an ‘identity’sequence and a ‘difference’ sequence. These maybe used on subsets of sequences and in further comparisons toidentify candidate sites involved in a distinct functional property.The program should prove a useful tool for biologists engagedin understanding sequence—function relationships.