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

Joint Genorne Institute, a sequencing centre in the USA.

Kb or Kbp

Kilobase or kilobase pair, region of DNA 1000 nucleotides long.


The KEGG (Kyoto Encyclopedia of Genes and Gen ornes) is a bioinformatics resource for linking genomes to life and the environment.

Linkage map

Genetic map produced using recombination values of genes other markers to identify the linear order and relative distance of these markers on a chromosome.

Local alignment

Sequence alignment which focuses on matching part of one sequence with part of another.


Lipopolysaccharides, large molecules containing a lipid and a polysaccharide linked by a covalent bond major components of the outer membrane of Gram negative bacteria; Induce strong immune responses in animals.


A certain kind of scatter-plot commonly used for microarray analysis where the intensity measurements from microarrays are transformed in a special way. The. x-axis corresponds to the absolute intensity of the spot (A-value), the y-axis corresponds to a measure of differential expression (M-value).


A data format used to transfer microarray data to public repositories (e.g. ArrayExpress). The MAGE-TAB format consists mainly of spread sheets, which can be represented as tabulator- or comma-separated files.


Marker-Assisted Selection; Selection of a genetic determinant of a trait of interest (e.g. productivity, disease resistance and quality) through the use of a marker (morphological, biochemical or one based on DNA/RNA variation).


Position with identical bases or amino acids in a sequence alignment.


Paired reads of the two ends of a cloned DNA molecule. Mate-pairs are often used by genome assembly programs to orient and order contigs, taking into account the distance between the ends of the DNA molecule and the orientation relationship of the sequences.


Multiple displacement amplification. Isothermal DNA amplification method using random hexarners and the DNA polymerase of bacteriophage Ø29.


High throughput analysis of the metabolites present in a cell type, a tissue or an organism and the modifications to metaholite pools under different conditions.

Metagenornics (or environmental sequenci

Application of genomic analysis, particularly high-throughput sequencing to environmental samples such as uncultured microbial communities.


Global analysis, usually by sequencing, of the expressed genetic information (gene transcripts) produced by the collection of organisms in an ecosystem.


Major Histocompatibility Complex;  A large genornic region playing an important role in the immune system, autoimmunity and reproductive success.


Small DNA stretches of a repeated core sequence of few base pairs (e.g. GT repeat units) that are highly polymorphic, particularly in terms of the number of repeated units. These are mainly used to create genetic maps.


Minimal Infai-mation About a Microarray Experiment. MIAME is a recommendation that was established by a joint group of microarray experts (the Microarray and Gene Expression Data society or MGED) and describes the minimal requirements for data and information that a submission to a public microarray database should contain. The aim is to make microarray data understandable and reproducible.


Minimum Information about a Metagenome Sequence.


Position with different bases or amino acids in a sequence alignment.

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