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Glossary
HMMs may include states modeling introns, exons, intergenic regions, start and stop
codons, splice signals, polyadenyation signals and ribosomal binding sites.
Homeodomain proteins a class of proteins characterized by the existence of a
specific motif, the homeodomain, which is primarily involved in DNA binding.
Homologue In order to describe the evolutionary relation of proteins, the terms
homology, orthology, and paralogy are used. In this context, homology means
that two proteins or sequences share a common ancestor. Two principal types of
homology can be distinguished (Orthology and Paralogy).
Horizontal (or lateral) gene transfer A process in which genes from one organism are integrated into the genome of a second organism (which may be very
distantly related to the first) and subsequently inherited with the rest of the genetic
material of the cell.
Hox cluster genomic array of Hox genes, which constitute a subgroup of homeodomain proteins. Spatial Hox gene expression during development tends to
correlate with the spatial arrangements of genes in the genomes of a broad panel
of animals. Hence, Hox clusters also serve as a paradigm to understand the
commonalities and changes during the evolution of animal body plans.
HSP high-scoring segment pair.
IMG The Integrated Microbial Genomes system.
INSDC International Nucleotide Sequence Database Collaboration. It consists of
the DDBJ (Japan), EMBL (Europe) and GenBank (USA) Nucleotide Sequence
Database. The three databases exchange new and updated data on a daily basis to
achieve optimal synchronization.
IUPAC International Union of Pure and Applied Chemistry. This nongovernmental organisation has developed a system of naming chemical elements
and their compounds such as amino acids or nucleotides.
JCoast Comparative Analysis and Search Tool.
JGI Joint Genome Institute, a sequencing centre in the USA.
KEGG The KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment.
Kb or Kbp kilobase or kilobase pair, region of DNA 1000 nucleotides long.
Linkage map Genetic map produced using recombination values of genes or other
markers to identify the linear order and relative distance of these markers on a
chromosome.
LPS Lipopolysaccharides; large molecules containing a lipid and a polysaccharide
linked by a covalent bond; major components of the outer membrane of Gramnegative bacteria; induce strong immune responses in animals.
Glossary
HMMs may include states modeling introns, exons, intergenic regions, start and stop
codons, splice signals, polyadenyation signals and ribosomal binding sites.
Homeodomain proteins a class of proteins characterized by the existence of a
specific motif, the homeodomain, which is primarily involved in DNA binding.
Homologue In order to describe the evolutionary relation of proteins, the terms
homology, orthology, and paralogy are used. In this context, homology means
that two proteins or sequences share a common ancestor. Two principal types of
homology can be distinguished (Orthology and Paralogy).
Horizontal (or lateral) gene transfer A process in which genes from one organism are integrated into the genome of a second organism (which may be very
distantly related to the first) and subsequently inherited with the rest of the genetic
material of the cell.
Hox cluster genomic array of Hox genes, which constitute a subgroup of homeodomain proteins. Spatial Hox gene expression during development tends to
correlate with the spatial arrangements of genes in the genomes of a broad panel
of animals. Hence, Hox clusters also serve as a paradigm to understand the
commonalities and changes during the evolution of animal body plans.
HSP high-scoring segment pair.
IMG The Integrated Microbial Genomes system.
INSDC International Nucleotide Sequence Database Collaboration. It consists of
the DDBJ (Japan), EMBL (Europe) and GenBank (USA) Nucleotide Sequence
Database. The three databases exchange new and updated data on a daily basis to
achieve optimal synchronization.
IUPAC International Union of Pure and Applied Chemistry. This nongovernmental organisation has developed a system of naming chemical elements
and their compounds such as amino acids or nucleotides.
JCoast Comparative Analysis and Search Tool.
JGI Joint Genome Institute, a sequencing centre in the USA.
KEGG The KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment.
Kb or Kbp kilobase or kilobase pair, region of DNA 1000 nucleotides long.
Linkage map Genetic map produced using recombination values of genes or other
markers to identify the linear order and relative distance of these markers on a
chromosome.
LPS Lipopolysaccharides; large molecules containing a lipid and a polysaccharide
linked by a covalent bond; major components of the outer membrane of Gramnegative bacteria; induce strong immune responses in animals.