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Comparing a mass-balance algorithm with a Bayesian regression analysis computer program for predicting serum phenytoin concentrations.

The ability of a mass-balance algorithm to predict non-steady-state phenytoin concentrations in neurosurgery patients was compared with that of Phenda, a computerized Bayesian regression analysis program. Fifty neurosurgery patients who had had two or more initial phenytoin serum concentrations measured at least 60 hours apart and at least 1 hour after any i.v. doses, with the second concentration being not more than twice and not less than half of the first, and who had had a third or final phenytoin measurement (for use in a prediction analysis) were evaluated. The patients' maximum rates of metabolism were calculated by using the two initial phenytoin concentrations and a mass-balance algorithm, and the third phenytoin concentration was predicted. The patients' demographics and phenytoin dosages and concentrations were entered into Phenda, which was used to predict the third phenytoin concentration. The ability of the two methods to predict the third concentration was evaluated by the method of Sheiner and Beal. Fifty observations from 48 patients were evaluated. The mass-balance algorithm had a positive prediction bias of 2.52 mg/L and a precision error of 5.08 mg/L, compared with 2.30 and 5.30, respectively, for Phenda. The difference in the results between the two methods was not significant. There was no significant difference between the mass-balance algorithm and Phenda in the ability to predict phenytoin concentrations.

Algorithms↗

DNASUN: a package of computer programs for the biotechnology laboratory.

The paper describes a new software package DNASUN developed for supporting gene engineering laboratories. The package provides a user-friendly interface for experimental researches and supports the traditional nucleotide/protein sequence analysis as well as physical mapping, sequencing, plasmid manipulations, optimal oligonucleotide probe selection and other common molecular biology procedures.

Biotechnology↗

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.

The information matrix database (IMD), a database of weight matrices of transcription factor binding sites, is developed. MATRIX SEARCH, a program which can find potential transcription factor binding sites in DNA sequences using the IMD database, is also developed and accompanies the IMD database. MATRIX SEARCH adopts a user interface very similar to that of the SIGNAL SCAN program. MATRIX SEARCH allows the user to search an input sequence with the IMD automatically, to visualize the matrix representations of sites for particular factors, and to retrieve journal citations. The source code for MATRIX SEARCH is in the 'C' language, and the program is available for unix platforms.

Base Sequence↗

CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.

A key concept in comparing sequence collections is the issue of redundancy. The production of sequence collections free from redundancy is undoubtedly very useful, both in performing statistical analyses and accelerating extensive database searching on nucleotide sequences. Indeed, publicly available databases contain multiple entries of identical or almost identical sequences. Performing statistical analysis on such biased data makes the risk of assigning high significance to non-significant patterns very high. In order to carry out unbiased statistical analysis as well as more efficient database searching it is thus necessary to analyse sequence data that have been purged of redundancy. Given that a unambiguous definition of redundancy is impracticable for biological sequence data, in the present program a quantitative description of redundancy will be used, based on the measure of sequence similarity. A sequence is considered redundant if it shows a degree of similarity and overlapping with a longer sequence in the database greater than a threshold fixed by the user. In this paper we present a new algorithm based on an "approximate string matching' procedure, which is able to determine the overall degree of similarity between each pair of sequences contained in a nucleotide sequence database and to generate automatically nucleotide sequence collections free from redundancies.

Algorithms↗

A computer program for the analysis of protein complex formation.

MOTIVATION: We needed an efficient way to explore the binding reactions leading to protein complexes of known composition and structure. RESULTS: A new program is described that allows the user to define a set of protein elements and to link these elements into an oligomeric 'ball-and-stick' assembly in a graphical interface. Once the structure of the oligomer has been defined, the program then employs a novel algorithm to deduce the binding reactions and intermediate complexes needed to make the oligomer from its starting protein components. The program also finds the equilibrium state of the system, using either default starting concentrations and Kd values or data supplied by the user.

Algorithms↗

A package of computer programs for handling taxonomic databases.

A package of programs is described which processes taxonomic data, suitable to use when preparing monographs, handbooks, Floras or Faunas, in which species or other taxa are described and identified. There is also an interactive program for specimen identification, and conversion routines which prepare data for numerical taxonomy (clustering and cladistics). The programs are equally suitable for botany or for zoology, or even for non-biological data.

Animal Population Groups↗

A computer program to display codon changes caused by mutagenesis.

A FORTRAN program for displaying the correspondence between codon changes and different possible base changes is presented. Changes of both single bases and dimers are considered. The user can specify the mutagenesis spectrum. Additionally, the user can choose whether or not to consider single or double events in a codon and whether or not to consider the possibility that the change of two bases (a dimer) can overlap a codon boundary. Furthermore, a variety of ways may be chosen to display and summarize the codon changes that can result from the specified mutagenesis. A user-supplied sequence or the genetic code table can be analyzed.

Codon↗

SPLICE, a computer program for automated extraction of information from GenBank sequence entries.

SPLICE, a software tool for the extraction of sequences from files in GenBank tape format, has been developed. The program can analyze the features table in this format and use any of the information provided to write the corresponding sequences into a standard sequence file format suitable for use with sequence analysis programs. Sequences that are present as several subsequent fragments in a single GenBank file, such as those encoding a peptide, can be spliced together by the program. Further, sequences that are present in more than one Genbank file, such as an exon which spans several different files, can also be spliced into one sequence. SPLICE runs under the MS/DOS and Unix operating systems, can be called as a sub-process by other programs and can process batches of files.

Animals↗

SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements.

SIGNAL SCAN is a program that has been developed to aid the molecular biologist in determining what eukaryotic transcription factor elements (and other significant elements) may exist in a DNA sequence under investigation. The program uses flatfile databases of these elements. SIGNAL SCAN is most useful for analyzing mammalian sequences due to the prevalence of mammalian elements in the database. Elements not found in the SIGNAL SCAN database may be entered by the user. SIGNAL SCAN uses both specific sequence elements derived from biochemical characterization and elements from derived consensus sequences to match against a user input DNA sequence. While any DNA sequence element matching an element in the SIGNAL SCAN database will be reported by the program, the determination of the biological relevance of the element is left up to the investigator.

Algorithms↗

ADEPT: a computer program for prediction of protein antigenic determinants.

ADEPT, a program that can be used for prediction of protein antigenic determinants from the amino acid sequence alone for the cases of humoral and cellular immune response, is described. Most methods presently utilized for this purpose are implemented in the program along with some original parameters for the case of humoral immune response. There is also a possibility to combine several methods for the case of humoral immune response, which provides a means to create new predictive methods. ADEPT also includes a literature-derived database of proteins in the SWISS-PROT standard with experimentally determined antigenic determinants, so the predictive ability of new methods can be assessed within the program and corresponding statistical information is calculated. ADEPT may be useful for solving various tasks involving the delineation of antigenic regions on proteins or characterization of peptide fragments, arising, for example, in protein engineering (e.g. selection of protein portions most suitable for insertion of peptide sequences that are antigenically active or possessing other desired characteristics), and in particular for construction of vaccines containing B- and/or T-cell epitopes, as well as for other problems of medico-biological research.

Algorithms↗