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
2R hypothesis

Hypothesis suggesting that the genomes of the early vertebrate lineage underwent two rounds of whole-genome duplications, reflected e.g. by the existence of 4 remnants of I-lox clusters.

Accession number

An identifier supplied by the curators of the major biological databases upon submission of a novel entry (usually sequence data) that uniquely identifies that database entry.


This technique produces DNA fragments that are separated by size (length of sequence) using polyacrylamide gel electrophoresis or capillary sequencers. Bands at a particular site on the gel (equivalent to alleles) are counted as being present or absent for the analysis.


All photosynthetic eukaryotes other than land plants.

Algal bloom

Rapid multiplication of one or a small number of algal species. In some cases the algae are toxic.


Overview of both differences and similarities between two or more DNA, RNA or protein sequences created by aligning residues that are putatively homologous. Gaps may be introduced to optimally align the sequences.


Acid Mine Drainage.


Application Programming Interface.


Bacterial artificial chromosome. a cloning vector carrying up to 300 kbp of insert sequence.


A svecific piece of DNA (usually Dart of the mitochondrial cytochrome coxidase sub unit l gene) is sequenced many times from different species. There are sufficient interspecies differences in this gene, for the sequence of DNA to act as a unique code for a species and therefore be used as a taxonomic aid.


The application of information technology to the field of molecular biology.


Programming networks to handle the most common file formats and tools that are used by bioinformaticians.


Programming network to handle the most common file formats and tools that are used by bioinformaticians.


“Basic Local Alignment Search Tool”, a well-known and established tool for finding homologue sequences in large sequence databases.


Community Cyberinfraestructure for advanced marine Microbial Ecology Research and Analysis.


The term “clone” can refer to a bacterium carrying a piece of cloned DNA, or to the cloned DNA itself.


EST sequences are clustered according to their sequence, so that they can be assembled afterwards. The set of all Clusters form a Cluster set.


The COG (Cluster of Orthologous Groups of proteins) database consists of 138.458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in the 66 genomes of unicellular organisms that were used for the database. The eukaryotic orthologous groups (KOGS) include proteins from 7 eukaryotic genomes.


Fish in a stock born in the same year.


The term “contig” comes from a shortening of the word “contiguous". It can be used to refer to the final product of a shotgun sequencing project. When individual lanes of sequence information are assembled to infer the sequence of the larger DNA piece, the product consensus sequence is called a “contig”.

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