Computer applications in the biosciences : CABIOS最新文献

Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap.

Availability: Seq-Gen can be obtained by WWW from http:/(/)evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html++ + or by FTP from ftp:/(/)evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.

Motivation: Efficient high-throughput genotyping experiments require the multiplexing of polymorphic markers, i.e. the use of multiple markers with non-overlapping allele size ranges in a single lane of a genotyping gel. The arrangement of such markers into sets can be facilitated by the availability of appropriate computer software.

Results: This article describes a program, Grouper, that automates the generation of marker sets for multiplexed genotyping experiments.

Availability: The software described in this article is available free of charge from the EBI software archive at (ftp://ftp.ebi.ac.uk/pub/software/unix).

Motivation: Secondary structure predictions based on the properties of individual residues, and sometimes on local interactions, usually fail to exceed 65% efficiency. Therefore, non-local, long-range interactions seem to be a significant cause of this limitation.

Results: In this paper, we apply approaches to localize highly interacting residues and clusters of residues involved in multiple non-local interactions, and test various secondary structure predictions on this separate subset to assess the effect of long-range interactions on the prediction efficiencies. It was found that only a marginal part of the failure of secondary structure predictions results from the presence of long-range interactions. Alternative possibilities are also discussed.

Present-day sequences are the result of long and complex pathways of evolution. Many of the features encoded in them are the result of a series of evolutionary processes, including selection, genetic drift, etc. Following this, protein families have a great amount of unexplored information that can be useful for many purposes beyond simple evolutionary studies. An index is presented here which permits the localization of regions showing an unexpected degree of variability or conservation. This index uses the information contained in sequence alignments and compares the observed over expected level of variability using tables for the relative likelihood of amino acid change.

Motivation: Genomic sequences from different organisms, even prokaryotic, have plenty of orphan ORFs, making necessary methods for the prediction of protein structure and function. The prediction of the presence of hydrophobic transmembrane (HTM) stretches is a valuable clue for this.

Results: The program. TransMem, based on a neural network and running on personal computers (either Apple Macintosh or PC, using Excel worksheets), for the prediction and distribution of amino acid residues in transmembrane segments of integral membrane proteins is reported. The percentage of residue predictive accuracy obtained for the set of proteins tested is 93%, ranging from 99.9% for the best to 71.7% for the worst prediction. The segment-based accuracy is 93.6%; 63.6% of the protein set match any of the predicted and observed segment locations.

Availability: TransMem is available upon request or by anonymous up: IP address: luz.uab.es, directory/pub/ TransMem. It is also placed on the EMBL file server (ftp:/(/)ftp.ebi.ac.uk/pub/software/mac/TransMem ).

Motivation: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for site-directed mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR).

Results: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region.

Availability: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/+ ++matchbox_submit.html or sent by e-mail to matchbox/biq.fundp.ac.be (help available by just mailing help).

Motivation: The principal motivation was to design an environment for the development of image-analysis applications which would allow the integration of independent modules into one frame and make available tools for their build-up, running, management and mutual communication.

Results: The system was designed as modular, consisting of the core and work modules. The system core focuses on overall management and provides a library of classes for build-up of the work modules, their user interface and data communication. The work modules carry practical implementation of algorithms and data structures for the solution of a particular problem, and were implemented as dynamic-link libraries. They are mutually independent and run as individual threads, communicating with each other via a unified mechanism. The environment was designed to simplify the development and testing of new algorithms or applications. An example of implementation for the particular problem of the analysis of two-dimensional (2D) gel electrophoretograms is presented. The environment was designed for the Windows NT operating system with the use of Microsoft Foundation Class Library employing the possibilities of C++ programming language.

Availability: Available on request from the authors.

Motivation: The increasing availability of biological databases on the World-Wide Web and hypertext links between them has made a wealth of information easily accessible to biologists. Additional retrieval capabilities can be achieved by storing explicitly specified biological relationships between different entities as discrete database entries.

Results: We have built CySPID, a prototype database about the cytoskeleton that explores the approach of explicitly representing biological relationships. The stored relationships are displayed along with other retrieved information, can be used to make hyperlinks to related entities, and can be used to search for entities with specified properties. CySPID is extensible in that new types of relationships may be created without altering the database schema.

Availability: CySPID is available for public use (http://ycmi.med.yale.edu/cyspid/). The CGI scripts used by CySPID are available upon request.