An access interface for the MS-DOS diskette format of GenBank(R), a gene sequence database

An interface program has been developed for users of MS-DOScomputers and the GenBank(R) gene sequence files in their disketteformat. With the program a user is able to produce keyword,author and entry name listings of GenBank items or to selectGenBank sequences for viewing, printing or decoding. The decodeoption uncompresses sequence data and yields a character filewhich has the format used on GenBank magnetic tapes. Programoptions are chosen by selecting items from command menus. Whilethe program is designed primarily for hard disk operation, italso allows users of diskette-based computers to work with GenBankfiles. Received on July 15, 1987; accepted on July 15, 1987     

A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes

A computer program has been written in FORTRAN 77 to locateon a protein sequence a region with optimum length and limiteddegeneracy in order to design artificial oligonucleotide probesfor use in molecular cloning. In addition the program checksfor regions of homology between this probe and any other basesequence found in nucleotide sequence data banks. There areoptions in the program to eliminate rare codons or to make preferentialchoices of bases in order to minimize the degeneracy of probes. Received on February 17, 1987; accepted on June 26, 1987     

FUGE: an analytical ultracentrifuge simulation for teaching purposes

An IBM-compatible microcomputer program for teaching purposesis described which simulates the operation of a sedimentationvelocity determination of a protein in an analytical ultracentrifugeusing schlieren optics. The program operates in speeded-up timeand simulates the major procedures which would need to be carriedout to operate such an instrument. The position of the sedimentingboundary can be observed at any time during the run, and upto six ‘photographs’ can be recorded for subsequentanalysis. Calculation of sedimentation coefficient, diffusioncoefficient and mol. wt can be made from a dot-matrix printout.Ten representative proteins are stored within the program, butprovision exists for user-supplied data. Received on June 25, 1987; accepted on September 9, 1987     

Matching relational patterns in nucleic acid sequences

We describe a program that efficiently searches sequence databanks for complex patterns where sites are linked by commonrelations such as identity, complementarity or span. Its algorithmis closer to those of automatic demonstration than to the finitestate machines used in fast pattern matching. The repertoryof relations can be enriched at will without rewriting the coreof the program. The program is written in Pascal-ISO and runson a microcomputer. Received on September 25, 1986; accepted on April 30, 1987     

AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA

A UGUR is a program to predict, display and analyze the three-dimensionalstructure of B-DNA. The user can choose one of six models topredict the helical parameters of a given sequence. These parametersare then used to generate the coordinates of the DNA model inthree-dimensional space (trajectory). The trajectory can bedisplayed and rotated on a graphics terminal The trajectoryand helical parameters can also be searched for bends and structuralhomologues. Received on August 17, 1987; accepted on December 31, 1987     

Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome

This paper describes software (written in Pascal and running on Macintosh computers) allowing localization of unknown DNA fragments from the Escherichia coli chromosome on the restriction map established by Kohara et al. (1987). The program identifies the segment's map position using a restriction pattern analysis obtained with all, or some, of the eight enzymes used by Kohara et al. (1987). Therefore, the sequenced genes available in the EMBL library may be localized on the E. coli chromosome restriction map. This allowed correction of the map (mainly by introducing missing sites in the published maps) at the corresponding positions. Analysis of the data indicates that there is only a very low level of polymorphism, at the nucleotide level, between the E. coli K12 strains used by the various laboratories involved in DNA sequencing. The program is versatile enough to be used with other genomes.     

Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions

A program has been developed for the modelling of modificationsin DNA ends, for the construction of ligated junctions, andfor the analysis in these junctions of new restriction enzymerecognition sequences. This program allows the analysis of restrictionenzyme specifities in ligated junctions of cohesive or bluntDNA ends. Cohesive ends are considered in their natural configurationor after modification by possible blunt-ending procedures. Theprogram also allows the modelling of partial filling-in for5'-single-stranded ends. This program has proven useful forthe design of sequences with new restriction sites or to predictor confirm the sequence of junctions created by the ligationof modified ends. Received on October 28, 1987; accepted on November 23, 1987     

PARA-SITE: a computer algorithm for rapidly analyzing the physical-chemical properties of amino acid sequences at sites of co- and post-translational protein processing

A new algorithm is presented which can be used to examine thephysical-chemical properties of amino acids at sites of co-orpost-translational processing. This algorithm has been incorporatedinto a computer program known as PARA-SITE. Thirty differentparameters can be studied for amino acids which occupy comparablepositions in naturally occurring proteins. PARA-SITE shouldaid in the design and interpretation of protein engineeringexperiments which seek to dissect structure/ activity relationships. Received on August 17, 1987; accepted on November 23, 1987     

Locating alignments with k differences for nucleotide and amino acid sequences

Given two sequences, a pattern of length m, a text of lengthn and a positive integer k, we give two algorithms. The firstfinds all occurrences of the pattern in the text as long asthese do not differ from each other by more than k differences.It runs in O(nk) time. The second algorithm finds all subsequencealignments between the pattern and the test with at most k differences.This algorithm runs in O(nmk) time, is very simple and easyto program. Received on August 12, 1987; accepted on December 31, 1987     

The antigenic index: a novel algorithm for predicting antigenic determinants

In this paper, we introduce a computer algorithm which can beused to predict the topological features of a protein directlyfrom its primary amino acid sequence. The computer program generatesvalues for surface accessibility parameters and combines thesevalues with those obtained for regional backbone flexibilityand predicted secondary structure. The output of this algorithm,the antigenic index, is used to create a linear surface contourprofile of the protein. Because most, if not all, antigenicsites are located within surface exposed regions of a protein,the program offers a reliable means of predicting potentialantigenic determinants. We have tested the ability of this programto generate accurate surface contour profiles and predict antigenicsites from the linear amino acid sequences of well-characterizedproteins and found a strong correlation between the predictionsof the antigenic index and known structural and biological data. Received on August 17, 1987; accepted on December 31, 1987     

Turbo Tree: a fast algorithm for minimal trees

A branch and bound algorithm is described for searching rapidlyfor minimal length trees from biological data. The algorithmadds characters one at a time, rather than adding taxa, as inprevious branch and bound methods. The algorithm has been programmedand is available from the authors. A worked example is givenwith 33 characters and 15 taxa. About 8 x 10¹² binary treesare possible with 15 taxa but the branch and bound program findsthe minimal tree in <5 min on an IBM PC. Received on January 15, 1987; accepted on February 23, 1987     

HERSIM: a microcomputer program designed to compute the limits of conversion for real homogeneous isothermal enzymic reactors

HERSIM is a program written in BASIC designed to aid the investigatorinterested in determining the substrate conversion in a realhomogeneous isothermal enzymic reactor, for various kineticequations. The program runs after tracer data relative to aDirac impulse to the reactor have been entered, and computesthe two limits of real conversion: total segregation and maximummixedness. The kinetic constants of the reacting system areinput as data, and the variation of conversion with reactortemperature between given limits is computed as accurately asrequested. Received on November 6, 1986; accepted on March 4, 1987     

Computer aided design of pellets for fixed-bed reactors performing Michaelis--Menten reactions

The problem of designing the pellet characteristics for existingfixed-bed reactors has been studied. The reactor is assumedto be a unidimensional, plug-flow, heterogeneous type. Threeparticle shapes, two intraparticle mass transfer mechanisms,two lands of film resistance to mass transfer and two poisoningpatterns have been considered. An economic balance to both productmarket price and pellet market cost was taken into account.An interactive program (HIMER) containing all these contributionswas thus developed, enabling the investigator to follow thereactor performance along the flow coordinate. Received on March 26, 1987; accepted on June 25, 1987     

Breeding program for the lesser kudu (Tragelaphus imberbis) in North America

The lesser kudu (Tragelaphus imberbis) has been kept in North American zoological parks since 1930 but has never been a common species in collections. In 1987 this population totaled 28 animals: 15 males and 13 females. A pedigree evaluation in 1987 of the existing population indicated that eight effective founders and one potential founder were represented in the North American herd. Three new potential founders from European captive populations were added to the population in 1987 to increase the number of existing founder lines to 12 animals. As this species is not endangered or threatened in its native habitat, it is not a high priority to qualify for designation as an SSP species. Because of this, the institutions holding lesser kudu in North America decided to join informally and draft a breeding program to better manage this small captive population. This program was designed to minimize inbreeding and equalize genetic representation of founder animals to maximize genetic diversity. It requires a shift in management philosophy to establish stable groups of breeding females at participating institutions while rotating appropriate breeder males through these herds in a controlled manner to ensure minimization of inbreeding and maximization of genetic diversity. It is hoped that this program can serve as a model for the management of other small captive populations of non-SSP species.     

A program for template matching of protein sequences

The matching of a template to a protein sequence is simplifiedby treating it as a special case of sequence alignment. Restrictionof the distances between motifs in the template controls againstspurious matches within very long sequences. The program usingthis algorithm is fast enough to be used in scanning large databasesfor sequences matching a complex template. Received on August 17, 1987; accepted on January 11, 1988     

A student-centred,problem-based curriculum: 5 years' experience.

In 1987, the University of Sherbrooke''s school of medicine implemented a student-centred, problem-based learning (PBL) curriculum. The experience of the first 5 years is reviewed; program goals, the schedule of learning activities, the instructional format and assessment of student learning are described. The new program is more demanding of teachers and requires better faculty training in pedagogy. No new financial resources have been available. The preclinical reform has led to revision of the clerkship, where sessions on clinical reasoning are now based on the PBL philosophy. Student reactions to the program are reported. The Sherbrooke experience has demonstrated that it is both possible and feasible to shift from a traditional to a problem-based curriculum.     

BCETM: a tool for software integration

The integration of software into special-purpose systems (e.g.for gene sequence analysis) can be a difficult task. We describea general-purpose software integration tool, the BCETM program,that facilitates assembly of VAX-based software into applicationsystems and provides an easy-to-use, intuitive user interface.We describe the use of BCE to integrate a heterogeneous collectionof sequence analysis tools. Many BCE design features are generallyapplicable and can be implemented in other language or hardwareenvironments. Received on May 13, 1987; accepted on October 2, 1987     

Hand-held computer program for field-capture and analysis of herbage yield and composition data using a modified dry-weight-rank and yield estimate method

A BASIC program is described which is used to collect, checkand analyse rank estimates of plant yield in the field. Theprogram operates in a portable, battery-powered Sharp PCI500Ahand-held computer than can be used in a field environment.Data are collected using a modified dry-weight-rank method andcomparative yield estimates. Much of the software is designedto trap incorrect data entry. Raw data or summary data may beprinted, displayed, and stored on cassette tape or transferredto another computer through a communications interface. Theprogram can be easily modified to run on other models of theSharp PC series or other portable computers that use a similarBASIC interpreter. Received on July 2, 1987; accepted on August 6, 1987     

A multiple alignment program for protein sequences

A program for the multiple alignment of protein sequences ispresented. The program is an extension of the fast alignmentprogram by Wilbur et al. (1984) into higher dimensions. Theuse of hash procedures on fragments of the protein sequencesincreases the speed of calculation. Thereby we also take intoaccount fragments which are present in some, but not in all,sequences considered. The results of some multiple alignmentsare given. Received on September 11, 1986; accepted on March 18, 1987     

A flexible method to align large numbers of biological sequences

Summary A method for the alignment of two or more biological sequences is described. The method is a direct extension of the method of Taylor (1987) incorporating a consensus sequence approach and allows considerable freedom in the control of the clustering of the sequences. At one extreme this is equivalent to the earlier method (Taylor 1987), whereas at the other, the clustering approaches the binary method of Feng and Doolittle (1987). Such freedom allows the program to be adapted to particular problems, which has the important advantage of resulting in considerable savings in computer time, allowing very large problems to be tackled. Besides a detailed analysis of the alignment of the cytochrome c superfamily, the clustering and alignment of the PIR sequence data bank (3500 sequences approx.) is described.