Glossary infobadge

This glossary contains a number of definitions  from the following publication:
J. M. Cock; Tessmar-Raible, K.; Boyen, C.; Viard, F. (Eds.), Introduction to Marine Genomics, vol. 1, 1st ed., Advances in Marine Genomics Vol. (Springer, 2010). Available from: http://www.springer.com/life+sciences/ecology/book/978-90-481-8616-7?cm_mmc=Google-_-Book%20Search-_-Springer-_-0

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Term Definition
Cryptic species

A cryptic species is a species that is reproductively isolated (or at least genetically distinct) from a second species but which resembles the second species so closely that both have traditionally been considered a single species.




Denaturing gradient gel electrophoresis. Molecular fingerprinting technique that separates PCR products based on sequence differences that result in distinctly different denaturing characteristics of the DNA.



Dye A

Chemical compound used to label biological material such as cDNA allowing it to be detected. Often fluorescent compounds are used.


Environmental Gene Tags.


Enzyme Linked lmmuno Sorbent Assay; Biochemical test to detect and quantify an antigen in a sample using a specific antibody.

Emulsion PCR

A technique for generating a clonally amplified piece of DNA in vitro along with a microbead, within a mineral oil emulsion.


An endosymbiont is an organism that lives within the body or cells of another organism. Endosymbiosis played an important in the evolution of the eukaryotes as mitochondria and plastids were derived from endosymbiotic organisms captured  by ancestral  eukaryotic cells.


Graphical user interface. A common means of interaction between humans and computers, which uses graphical representations of data and offers user interaction via pointing devices (e.g. mouse).


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.

Homeodomain proteins

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).

Horizontal (or lateral) gene transfer

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.

Hox cluster

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.


The Integrated Microbial Genomes system.


International Nucleotide Sequence Database Collaboration. It consists of the DDBJ (Japan), EMJ3L (Europe) and GenBank (USA) Nucleotide Sequence Database. The three databases exchange new and updated data on a daily basis to achieve optimal synchronization.


International Union of Pure and Applied Chemistry. This non-governmental organisation has developed a system of naming chemical elements and their compounds such as amino acids or nucleotides


Comparative Analysis and Search Tool.

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