BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

**Definition:** This place covers:

Methods or systems for genetic or protein-related data processing in computational molecular biology.

Computational processing of data related to nucleic acids, proteins, peptides, or amino acids.

Bioinformatics methods or systems where the digital data processing is inherent or implicit, although not explicitly mentioned.

**Glossary:** - systems biology: Simulation and mathematical modelling of relationships and interactions between molecular entities in sub-cellular systems integrating genetic and/or protein-related data to describe the dynamic behaviour of, for example, protein-protein/protein-ligand interactions, regulatory networks and metabolic networks - phylogeny: Reconstruction of an evolutionary development and history of a species or higher taxonomic grouping of organisms; typically represented as a phylogenetic tree; methods for creating phylogenetic trees - phylogenetic tree: Tree-like graphical representation of phylogenetic relationships - molecular structure: 2-dimensional or 3-dimensional arrangement of atoms, groups of atoms or domains in nucleic acids, proteins, peptides and amino acids - structure alignment: Form of alignment to establish structural and functional equivalences between two or more proteins based on their secondary or tertiary structures - protein folding: Process by which a polypeptide chain folds into a specific 3-dimensional structure - domain: Domain of a protein is an element of the overall molecular structure that is self-stabilising and often folds independently of the rest of a polypeptide chain - drug targeting: Drug design strategy aiming at optimising the properties of a medicinal compound, based on the 3-dimensional structure of a target, for delivery to a particular tissue or organ in the body - functional genomics: Experimental analyses aiming at assessing the function of genes in determining traits, physiology and/or development of an organism, making use of computational and high-throughput technologies - proteomics: Large-scale study of the functions of proteins and their interactions with other molecular entities in a biological system - genotype: Genetic makeup or profile of an organism with respect to a trait - ploidy: Number of sets of chromosomes in a cell/cells of an organism - allele: Alternative form of a gene (one member of a pair) that is located at a specific position (locus) on a specific chromosome - snp: Single nucleotide polymorphism: a DNA sequence variation that involves a change in a single nucleotide and is commonly present in a part of a population - motif: Specific nucleotide or amino acid sequence pattern - population genetics: Study of genetic variation and genetic evolution of populations - linkage disequilibrium: Tendency of alleles located close to each other on the same chromosome to be inherited together - mutagenesis: Process by which the genetic information of an organism is changed, resulting in a mutation - gene expression: Process by which proteins are made or transcribed from the instructions encoded in DNA - gene expression profiling: Determination of the pattern of genes expressed, i.e. transcribed, under specific circumstances or in a specific cell line - probe design and optimisation for microarrays: Designing and selecting (i) optimal, highly specific probes, e.g. oligonucleotides, cDNA, fragments for hybridisation experiments with microarrays and (ii) optimal sets of probes, e.g. oligonucleotides, cDNA, to be chemically attached to a solid support to form an array - microarray: Plurality of nucleic acid probes attached to a substrate, which form an ordered pattern - sequence alignment: Process of comparing nucleic or amino acid sequences, generally by a linear alignment in such a way that equivalent positions in adjacent sequences are brought into the correct alignment with each other by introducing insertions in suitable positions, in order to identify similarities and/or differences amongst the compared sequences - sequence assembly: Method by which linear portions of sequence information are assembled to obtain full length gene sequence data - in silico: Performed on a computer or via computer simulations - ontology: Classification methodology for formalising a subject's knowledge in a structured and controlled vocabulary