380
Glossary
BioJava, BioPerl Programming frameworks to handle the most common file
formats and tools that are used by bioinformaticians.
BLAST “Basic local alignment search tool”, a well-known and established tool for
finding homologue sequences in large sequence databases.
CAMERA Community Cyberinfrastructure for Advanced Marine Microbial
Ecology Research and Analysis.
Clone the term “clone” can refer to a bacterium carrying a piece of cloned DNA,
or to the cloned DNA itself.
Clustering EST sequences are clustered according to their sequence, so that they
can be assembled afterwards. The set of all Clusters form a Clusterset.
COG/KOG 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.
Cohort Fish in a stock born in the same year.
Contig 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”.
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.
ddNTP dideoxy-nucleotide.
DGGE 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.
dNTP deoxy-nucleotide.
Dye A chemical compound used to label biological material such as cDNA
allowing it to be detected. Often fluorescent compounds are used.
EGT Environmental Gene Tags.
ELISA Enzyme Linked Immuno 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.
Endosymbiosis An endosymbiont is an organism that lives within the body or
cells of another organism. Endosymbiosis played an important in the evolution
Glossary
BioJava, BioPerl Programming frameworks to handle the most common file
formats and tools that are used by bioinformaticians.
BLAST “Basic local alignment search tool”, a well-known and established tool for
finding homologue sequences in large sequence databases.
CAMERA Community Cyberinfrastructure for Advanced Marine Microbial
Ecology Research and Analysis.
Clone the term “clone” can refer to a bacterium carrying a piece of cloned DNA,
or to the cloned DNA itself.
Clustering EST sequences are clustered according to their sequence, so that they
can be assembled afterwards. The set of all Clusters form a Clusterset.
COG/KOG 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.
Cohort Fish in a stock born in the same year.
Contig 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”.
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.
ddNTP dideoxy-nucleotide.
DGGE 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.
dNTP deoxy-nucleotide.
Dye A chemical compound used to label biological material such as cDNA
allowing it to be detected. Often fluorescent compounds are used.
EGT Environmental Gene Tags.
ELISA Enzyme Linked Immuno 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.
Endosymbiosis An endosymbiont is an organism that lives within the body or
cells of another organism. Endosymbiosis played an important in the evolution