MOTIVATION: Interpretation of high-throughput gene expression profiling requires a knowledge of the design principles underlying the networks that sustain cellular machinery. Recently a novel approach based on the study of network topologies has been proposed. This methodology has proven to be useful for the analysis of a variety of biological systems, including metabolic networks, networks of protein-protein interactions, and gene networks that can be derived from gene expression data. In the present paper, we focus on several important issues related to the topology of gene expression networks that have not yet been fully studied. RESULTS: The networks derived from gene expression profiles for both time series experiments in yeast and perturbation experiments in cell lines are studied. We demonstrate that independent from the experimental organism (yeast versus cell lines) and the type of experiment (time courses versus perturbations) the extracted networks have similar topological characteristics suggesting together with the results of other common principles of the structural organization of biological networks. A novel computational model of network growth that reproduces the basic design principles of the observed networks is presented. Advantage of the model is that it provides a general mechanism to generate networks with different types of topology by a variation of a few parameters. We investigate the robustness of the network structure to random damages and to deliberate removal of the most important parts of the system and show a surprising tolerance of gene expression networks to both kinds of disturbance.

MOTIVATION: Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. RESULTS: We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

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: When evaluating the results of a sequence similarity search, there are many situations where it can be useful to determine whether sequences appearing in the results share some distinguishing characteristic. Such dependencies between database entries are often not readily identifiable, but can yield important new insights into the biological function of a gene or protein. RESULTS: We have developed a program called CBLAST that sorts the results of a BLAST sequence similarity search according to sequence membership in user-defined 'clusters' of sequences. To demonstrate the utility of this application, we have constructed two cluster databases. The first describes clusters of nucleotide sequences representing the same gene, as documented in the UNIGENE database, and the second describes clusters of protein sequences which are members of the protein families documented in the PROSITE database. Cluster databases and the CBLAST post-processor provide an efficient mechanism for identifying and exploring relationships and dependencies between new sequences and database entries.

Profile searches using aligned short protein blocks are an effective method for identifying putative protein functions. An algorithm is presented that accelerates block searches by a factor 2-5 with only limited lack of sensitivity; this algorithm is particularly suited for application in large-scale genome research.

A tool is presented that helps to find biological functions for new protein sequences. Running on any Macintosh computer system, MacPattern provides a unique combination of different algorithms, speed and user-friendliness. It supports searches for protein patterns using the PROSITE database, protein block searches with the BLOCKS database, and the identification of statistically significant protein segments. MacPattern allows batch processing of sequences and automatic translations of nucleotide sequence data. It is particularly suited for genome analysis or cDNA sequencing projects.

A new utility program, MSU, is described that simplifies the use of electronic mail servers for sequence analysis. Service descriptions are defined in external control files which can be changed without affecting the main program. This approach makes MSU a highly flexible tool that allows easy modification, extension and customization of service descriptions to suit users' personal requirements.

A new program, BlockSearch, is described that allows biologists to search protein sequences against the BLOCKS database of aligned protein blocks by converting these blocks to site-specific scoring matrices. It thus complements existing tools for standard similarity searches and pattern searches which aid in elucidating the function of newly determined protein-coding sequences. The speed of the program and the existence of a command-line interface render BlockSearch particularly interesting for the batch analysis of many new sequences, such as collections of expressed sequence tags. Although written primarily for Digital's Alpha and VAX systems, the code is easily portable to other platforms.

This paper describes a system of generally applicable index files provided on the EMBL sequence databases CD-ROM to facilitate the development of front-end software to the sequence databases available on this CD-ROM. The index files are used by a new versatile and user-friendly database retrieval program for the Apple Macintosh, EMBL-Search, which allows the easy construction of complex database queries. EMBL-Search utilizes cross-reference information contained in the databases to support navigation between different information resources. The ability to run EMBL-Search on a local computer network accessing a shared database CD-ROM makes its use particularly cost effective.

MacP12, a program for the Apple Macintosh, allows simultaneous plotting of two protein property profiles selectable from 12 built-in amino acid property scales. Various parameters such as the region to be analyzed, the size of the sliding window, the weighting function and the size of the graphical output can be easily adjusted by the user, which makes this program appropriate for diverse research questions. Since built-in scales can be simply exchanged, MacP12 is adaptable to the specific needs of the individual user.

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.

MacT is a set of programs for the Apple Macintosh to construct and evaluate unrooted trees derived from amino acid sequences using a distance matrix method. Programs are designed on a 'one program--one task' basis for (i) determining the branching order in trees consisting of four or five species and calculating various statistical measures, (ii) calculating statistical measures for all possible topologies of unrooted trees and (iii) generating and evaluating trees derived from bootstrapped samples. With four auxiliary programs unrooted trees can be built for maximal 26 species, and the robustness of topologies be tested by bootstrapping.

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

A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; conversion mechanisms will transform binary files to ASCII to allow mail transfer. This service will also help authors to distribute their software conveniently.