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

Post-transcriptional modification. Alterations made to pre-mRNA before it leaves the nucleus and becomes mature mRNA.


Massively parallel DNA sequencing technique without the requirement of a prior cloning of the DNA.


Quantitative real-time reverse-transcription PCR. A PCR-based assay, which involves the direct measurment of the incorportation of a fluorescent dye into the PCR product. The level of fluorescence is a direct reflection on the amount of prduct present. By comparing the point in the PCR reaction where the reaction enters the log phase of replication for a control and a treated sample and determining the difference between the two, a measure of the change in relative gene expression caused by the treatment is determined.


Quantitative Trait Loci; A region of a chromosome that is associated with a particular measurable trait (see also eQTL).


Random Amplification of Polymorphic DNA; DNA fragments randomly amplified by PCR from genomic DNA with short primers (8-12 nucleotides) of arbitrary nucleotide sequence.


Rapid Annotation using Subsystem Technology.


A repetition of the same experimental measurement, The replicate can either be technical, where the same biological extract is analyzed twice, eg. by using the same mRNA for multiple microarrays; or it can be a biological replicate, when for example sample material is harvested from different individuals grown under the same conditions.


An oligonucleotide attached to the surface of a microarray.

RNA interference (RNAI)

A genetic mechanism in which double-stranded RNA is cleaved into small fragments and acts a signal to either initiate the degradation of a complementary messenger RNA or to interfere with its translation.


Reactive Oxygen species; Small molecules or ions formed by the incomplete one-electron reduction of oxygen; ROS contribute to oxidative stress/damage of DNA, lipids (oxidations of polydesaturated fatty acids), proteins (oxidations of amino acids) and inactivate specific enzymes (oxidation of co-factors).


Serial Analysis of Gene Expression. A high-throughput method to measure gene-expression by sequencing. Short fragments (tags) are generated from cDNA, which are then ligated to form long concatenated sequences, and, sequenced.


A two-dimensional plot where each measurement value is depicted by a single dot. Scatter-plots are often used to inspect data distributions.


Sodium dodecylsulphate - polyacrylamide gel electrophoresis; method used to separate proteins involving electrophoresis on an acrylamide gel.

Seaweed Brown

Red or green macroalgae.

Secondary endosymbiosis

An event in which a eukaryotic cell enslaves another eukaryotic cell that possesses a plastid derived from a primary endosymbiosis (see also endosymbiosis and primary endosymbiosis).

Sequence trace file

Raw sequence data in the form of a chromatogram from a Sanger sequencing reaction. The NCBI Trace Archive (http://www.ncbi.nlm.nih.gov.gate1.inist.fr/Traces/home/) and the Ensembl Trace Server (http://trace.ensembl.org/) are a public repositories for this sort of data.

Short Read Archive (SRA)

An NCBI database that stores raw data from sequencing platforms such as the Roche 454 System.


A single EST sequence that does not cluster with other ESTs.


Single-nucleotide polymorphism; particular sites (base pairs) in a sequence that are polymorphic and can be used as markers.


Self Organizing Maps.

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