What is bioinformatics? A proposed definition and overview of the field

Background: The recent flood of data from genome sequences and functional g enomics has given rise to now field, bioinformatics, which combines element s of biology and computer science. Objectives: Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcr iptional regulatory systems. Methods. Our definition is as follows: Bioinformatics; is conceptualizing b iology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as ap plied moths, computer science, and statistics) to understand and organize t he information associated with these molecules, on a large-scale. Results and Conclusions: Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecula r structures, genome sequences, and the results of functional genomics expe riments (eg expression data). Additional information includes the text of s cientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a w ide range of computational techniques including sequence and structural ali gnment, database design and data mining, macromolecular geometry, phylogene tic tree construction, prediction of protein structure and function, gene f inding, and expression data clustering. The emphasis is on approaches integ rating a variety of computational methods and heterogeneous data sources. F inally, bioinformatics is a practical discipline. We survey some representa tive applications, such as finding homologues, designing drugs, and perform ing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.