Glossary
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Spot/feature 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.
SSR Simple Sequence Repeat; also known as microsatellite (see definition above).
SteN Statistical electronic Northern blot.
SVM 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.
Synteny 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).
Target In a microarray experiment, the target is labelled population of molecules
corresponding to the RNA or DNA extracted from mixtures of cells, tissues, cell
cultures or other samples. This labelled population of molecules is often referred to
erroneously as the probe.
TC Tentative Consensus Sequence. EST sequences can be clustered together using
assembly programs to form TCs.
Tertiary endosymbiosis An event in which a eukaryotic cell enslaves another
eukaryotic cell that possesses a plastid derived from a secondary endosymbiosis
(see secondary endosymbiosis). This has occurred several times in the dinoflagellates, and the captured plastid is thought to have replaced a pre-existing secondary
plastid (see also endosymbiosis).
TETRA A tool that can be used to calculate, how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints
about the relatedness of DNA sequences.
TGICL TIGR Gene Index Clustering tools.
Third Party annotation (TPA) sequence database A database designed to capture experimental or inferential results that support submitter-provided annotation
for sequence data that the submitter did not directly determine but can be derived
from DDBJ/EMBL/GenBank primary data.
Transcriptomics High-throughput analysis of the mRNA transcripts present in a
cell type, a tissue or an organism.
387
Spot/feature 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.
SSR Simple Sequence Repeat; also known as microsatellite (see definition above).
SteN Statistical electronic Northern blot.
SVM 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.
Synteny 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).
Target In a microarray experiment, the target is labelled population of molecules
corresponding to the RNA or DNA extracted from mixtures of cells, tissues, cell
cultures or other samples. This labelled population of molecules is often referred to
erroneously as the probe.
TC Tentative Consensus Sequence. EST sequences can be clustered together using
assembly programs to form TCs.
Tertiary endosymbiosis An event in which a eukaryotic cell enslaves another
eukaryotic cell that possesses a plastid derived from a secondary endosymbiosis
(see secondary endosymbiosis). This has occurred several times in the dinoflagellates, and the captured plastid is thought to have replaced a pre-existing secondary
plastid (see also endosymbiosis).
TETRA A tool that can be used to calculate, how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints
about the relatedness of DNA sequences.
TGICL TIGR Gene Index Clustering tools.
Third Party annotation (TPA) sequence database A database designed to capture experimental or inferential results that support submitter-provided annotation
for sequence data that the submitter did not directly determine but can be derived
from DDBJ/EMBL/GenBank primary data.
Transcriptomics High-throughput analysis of the mRNA transcripts present in a
cell type, a tissue or an organism.