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

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.


A spore-producing plant.


A small area on the surface of a microarray containing a defined probe. Features can be produced using a spotter or by direct synthesis of oligonucleotides on the substrate.


Simple Sequence Repeat; also known as microsatellite.


Statistical electronic Northern blot.


Support Vector Machine, high performance machine learning technique that has been used to improve classification accuracy in biological applications such as gene prediction, detection of protein family members, RNA and DNA binding proteins and the functional classification of gene expression data. SVMs can solve non-linear classification problems by learning an optimally separating hyperplane in a higher-dimensional feature space. By use of non-linear kernel functions such as a Gaussian kernel, complex and non-linear decision functions can be realised.


Evolutionary preservation of the order of genes in a genomic region that indicates that this order also reflects the arrangement of genes in the last common ancestor of two compared species. Subdivided into macro-synteny (conserved aspects on the chromosomal level) and micro-synteny (local, gene-by-gene synteny).

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