"Phylogenetic profiling" is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence-absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying functional equivalence between two genes, is a critical and nontrivial step and largely explains why previous work in this area has mainly focused on using presence-absence profiles in prokaryotic species. Here, we demonstrate that eukaryotic genomes have a high proportion of multigene families whose phylogenetic profile distributions are poor in presence-absence information content. This feature makes them prone to orthology mis-assignment and unsuited to standard profile-based prediction methods. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies are subclustered at ten levels of sequence identity-from 30% to 100%-and phylogenetic profiles built at each level. All the profiles are compared using normalised Euclidean distances to identify those with correlated changes in their domain copy number. We demonstrate that two protein families will "auto-tune" with strong co-evolutionary signals when their profiles are compared at the similarity levels that capture their functional relationship. Our method finds functional relationships that are not detectable by the conventional presence-absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes.

At UCL we have developed several automated protocols for generating protein family resources (CATH; Gene3D). These resources can be used to perform comparative genome analyses in order to understand the evolution of protein families. Also to identify biologically and/or medically interesting families for which no structural data currently exists and which may therefore be important targets for structure genomics initiatives.The CATH domain structure database, established by Orengo and Thornton in 1993, now contains a significant proportion of protein structures from the PDB clustered into 1400 evolutionary families. Relationships have been identified using robust structure comparison methods (SSAP, CATHEDRAL). We have also benchmarked and optimised various 1D-profiles and HMM based protocols for assigning genome sequences to families within the resource (e.g. SAM-T99, SAMOSA, CATH-ISL).In this way we can assign structural data to a large proportion (up to 60%) of whole or partial sequences in completed genomes and >80% of genes coding for enzymes and other proteins in biochemical pathways. However, in order to include all families regardless of whether their structure is known or not, a new protein family resource has been developed (Gene3D). In Gene3D, complete genes have been clustered according to sequence similarity alone, using a robust clustering method (Pfscape). 120 completed genomes from all kingdoms have been clustered into 220,000 gene families, 70,000 of which contain 2 or more sequences. Subsequently, we have labelled those gene families for which CATH structural or Pfam functional domain annotations can be provided for all or part of the gene.Preliminary analysis of the genome annotations reveals that a significant proportion (up to 70%) of CATH annotated genes or gene regions in genomes are assigned to domain families that are common to all three kingdoms of life. However, only 20% of the genome sequences are assigned to gene families common to all kingdoms. Since a large proportion of these genes are multidomain proteins this supports the view that a great deal of functional diversity within the genomes has been achieved by combining domain modules in different ways.In collaboration with Professor Janet Thornton, we have analysed a subset of 56 bacterial genomes to determine the recurrence of specific domain structure families within the genomes. This revealed a small but essential group of universal, and in some cases, highly recurring domain families. For some size-dependent families, domain recurrence is highly correlated with increase in genome size, whilst in other size-independent families no correlation is observed. Statistical analysis allowed us to distinguish three groups. Within the size-dependent families we differentiated two groups: linearly-distributed and non-linearly-distributed. Functional annotation using the COGs revealed that these domains were predominantly involved in metabolism and regulation, respectively. Whilst a third group of Evenly-distributed size independent domains are primarily involved in protein translation and biosynthesis.By mapping CATH and Pfam domains families onto all the genome sequences in Gene3D we observe that a few hundred highly recurrent families are dominating at least 50% of whole or partial genome sequences. Many of these families are common to both prokaryotes and eukaryotes and are performing essential generic functions. In many of the largest families, significant divergence in sequence has been accompanied by modifications in structure and function. Targetting representatives in these families for structure determination will allow the structure genomics initiatives to map both fold and function space and reveal the mechanisms by which divergence in protein families promotes evolution of new functions.

This paper describes the hardware and software architecture of a gateway between an Ethernet-style local area network called Strathnet and an X.25 packet switched network (British Telecom's PSS). The hardware is based on a Motorola 68000 processor using the VME bus, and peripheral boards based on an 8-bit 68120/1 processor for the local network and the X.25 interfaces. The software is layered from the low-level executive, through the three X.25 levels and the transport layer, and through the corresponding layers on the local network side, to the bridging software itself. Both hardware and software are designed so that the system can be a general-purpose gateway: for example, the local area network peripheral board could be replaced by a ring type interface, and the software within the local network layers could similarly be replaced.