9 Genomic Techniques and How to Apply Them to Marine Questions
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in Overbeek et al. (1999) to infer functional coupling of genes and thereby generate
additional evidence for functional annotation. Especially, if a gene with unknown
function is found in a conserved cluster among several genomes, this contextual
information can support a potential gene function (Tamames et al. 1997).
9.3.4.4 Existing Resources for Comparative Analyses
A variety of annotation systems have been developed to support the process of
genome annotation (see Section 9.3.3.2). With the availability of more than 1,000
completely sequenced genomes the comparative genome annotation strategy has
become of major interest. It incorporates existing genomic data from related or all
available genomes for the annotation of a novel genome. Here we present some
annotation systems that support this strategy as well as relevant ontologies and
databases.
MAGPIE: MAGPIE is an annotation system developed by Gaasterland et al.
(2000). It provides a graphic interface that annotators can use to navigate a genome
and it assists in automated data collection, analysis, and annotation. The system
uses the internal HERON tool to generate automated annotations based on evidence
from homology searches. The decision process of a human annotator is modelled in
a protocol that tries to select the best annotation from the description lines of high
scoring matching sequences.
ERGO: The ERGO genome analysis and discovery suite integrates data from
genomics, biochemistry, high-throughput expression profiling, genetics, and peerreviewed journals (Overbeek et al. 2003). 500 genomes at various levels of
completion have been integrated into the system. The functional assignment of
genes is supported by evidence derived from comparative analysis including coregulation, fusion events, chromosomal neighbourhood of functionally related
genes. Reconstructions of cellular pathways are contained in the database for
genomes from all three domains of life. The system is no longer publicly available
and is only accessible through a fee-based subscription.
The SEED: The SEED (Overbeek et al. 2004) system provides the functionality
to annotate the exponentially growing number of completely sequenced genomes.
It is an open source successor to the commercial WIT (Overbeek et al. 2000)
and ERGO annotation systems. The SEED system replaces the one-genome-at-atime annotation strategy with an approach involving simultaneous annotation of all
available genomes. The annotation process is supported by comparative analyses.
The sequences of organisms that are available to the public are present in the
system’s database and an all-against-all similarity matrix for the genomic features
is pre-computed and allows the detection and visualisation of chromosomal clusters
and functional coupling of genes. Furthermore, the pre-computed similarity information present in the database enables the annotator to find sets of orthologous
genes and annotate them consistently across the complete set of organisms. The
system also provides functionality to organize related genes on a higher level. The
SEED system was the first to introduce the concept of subsystems (Overbeek et al.
2005).
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in Overbeek et al. (1999) to infer functional coupling of genes and thereby generate
additional evidence for functional annotation. Especially, if a gene with unknown
function is found in a conserved cluster among several genomes, this contextual
information can support a potential gene function (Tamames et al. 1997).
9.3.4.4 Existing Resources for Comparative Analyses
A variety of annotation systems have been developed to support the process of
genome annotation (see Section 9.3.3.2). With the availability of more than 1,000
completely sequenced genomes the comparative genome annotation strategy has
become of major interest. It incorporates existing genomic data from related or all
available genomes for the annotation of a novel genome. Here we present some
annotation systems that support this strategy as well as relevant ontologies and
databases.
MAGPIE: MAGPIE is an annotation system developed by Gaasterland et al.
(2000). It provides a graphic interface that annotators can use to navigate a genome
and it assists in automated data collection, analysis, and annotation. The system
uses the internal HERON tool to generate automated annotations based on evidence
from homology searches. The decision process of a human annotator is modelled in
a protocol that tries to select the best annotation from the description lines of high
scoring matching sequences.
ERGO: The ERGO genome analysis and discovery suite integrates data from
genomics, biochemistry, high-throughput expression profiling, genetics, and peerreviewed journals (Overbeek et al. 2003). 500 genomes at various levels of
completion have been integrated into the system. The functional assignment of
genes is supported by evidence derived from comparative analysis including coregulation, fusion events, chromosomal neighbourhood of functionally related
genes. Reconstructions of cellular pathways are contained in the database for
genomes from all three domains of life. The system is no longer publicly available
and is only accessible through a fee-based subscription.
The SEED: The SEED (Overbeek et al. 2004) system provides the functionality
to annotate the exponentially growing number of completely sequenced genomes.
It is an open source successor to the commercial WIT (Overbeek et al. 2000)
and ERGO annotation systems. The SEED system replaces the one-genome-at-atime annotation strategy with an approach involving simultaneous annotation of all
available genomes. The annotation process is supported by comparative analyses.
The sequences of organisms that are available to the public are present in the
system’s database and an all-against-all similarity matrix for the genomic features
is pre-computed and allows the detection and visualisation of chromosomal clusters
and functional coupling of genes. Furthermore, the pre-computed similarity information present in the database enables the annotator to find sets of orthologous
genes and annotate them consistently across the complete set of organisms. The
system also provides functionality to organize related genes on a higher level. The
SEED system was the first to introduce the concept of subsystems (Overbeek et al.
2005).