title: Variation and evolution of biomolecular systems: searching for functional relevance.
abstract: The availability of genome sequences and functional genomics data from multiple species enables us to compare the composition of biomolecular systems like biochemical pathways and protein complexes between species. Here, we review small- and large-scale, "genomics-based" approaches to biomolecular systems variation. In general, caution is required when comparing the results of bioinformatics analyses of genomes or of functional genomics data between species. Limitations to the sensitivity of sequence analysis tools and the noisy nature of genomics data tend to lead to systematic overestimates of the amount of variation. Nevertheless, the results from detailed manual analyses, and of large-scale analyses that filter out systematic biases, point to a large amount of variation in the composition of biomolecular systems. Such observations challenge our understanding of the function of the systems and their individual components and can potentially facilitate the identification and functional characterization of sub-systems within a system. Mapping the inter-species variation of complex biomolecular systems on a phylogenetic species tree allows one to reconstruct their evolution.
authors.affiliation: Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands. m.huynen@cmbi.kun.nl
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Berend
authors.initials: B
authors.lastname: Snel
mesh_terms: D019143:Evolution, Molecular; D014644:Genetic Variation; D046912:Multiprotein Complexes / Q000235:genetics*; D010802:Phylogeny; D011485:Protein Binding / Q000235:genetics
chemical_list: D046912:Multiprotein Complexes