Hidden Markov Models (HMMs) allow the integration of diverse sequence features into a coherent, probabilistic framework. For the task of gene identification,  HMMs may include states modeling introns, exons, intergenic regions, start and stop codons, splice signals, polyadenyation signals and ribosomal binding sites.

A class of proteins characterized by the existence of a specific motif, the homeodomain, which is primarily involved in DNA binding.

In order to describe the evolutionary relation of proteins, the terms homology, orthology, and paralogy are used. In this context, homology means that two proteins or sequences share a common ancestor. Two principal types of homology can be distinguished (Orthology and Paralogy).

A process in which genes from one organism are integrated into the genome of a second organism (which may be very distantly related to the first) and subsequently inherited with the rest of the genetic material of the cell.

Genomic array of Hox genes, which constitute a subgroup of homeodomain proteins. Spatial Hox gene expression during development tends to correlate with the spatial arrangements of genes in the genomes of a broad panel of animals. Hence, Hox clusters also serve as a paradigm to understand the commonalities and changes during the evolution of animal body plans.

High-scoring segment pair.