56
A. Meyerdierks and F.O. Glöckner
designed for metagenome analysis is currently being developed and will be available
at http://metagenomics.ics.nmpdr.org
2.4.5 Annotation Systems for Local Installation
The arguments for installing an annotation system locally are mainly an improved
flexibility in handling and visualizing the data (Gans and Wolinsky 2007). After
the first round of data mining using web-based annotation systems, users normally
ask for custom tailored views on their data. To deal with such demands, full access
to the databases and tools is required. Since the advent of genomics at the beginning of the 1990s several annotation systems have been made available for local
installation. The most prominent are MAGPIE (Gaasterland and Sensen 1996),
PEDANT Pro (Frishman et al. 2001), WIT/ERGO (Overbeek et al. 1999, 2000)
and ARTEMIS (Rutherford et al. 2000). Currently, one of the most advanced is the
recently developed GenDB system (Meyer et al. 2003) which has been adopted by
the Networks of Excellence “Marine Genomics Europe” as their standard platform
for data processing and annotation.
Without going into details about the pros and cons of the different annotation
systems (an overview can be found in Stothard and Wishart 2006), we would like
to suggest that the data model and versatility of GenDB is the most appropriate
for the emerging demands of metagenomics. Starting with gene prediction, several options can currently be chosen in GenDB: 1. to run single gene finders such
as Glimmer (Delcher et al. 2007), Critica (Badger and Olsen 1999) or 2. to use a
combination of two gene finders united in the tool Reganor (McHardy et al. 2004).
Exchanging the preconfigured gene predictors by MetaGene or combined systems
(Bauer et al. 2006) can be done easily using a local installation. The standard tools
and databases for providing functional observations for the predicted genes can be
found in Table 2.1. Information about the location of a protein can be procured by
Table 2.1 Standard tools and databases providing functional observations
Tool
Databases
References
BLASTn
GenBank
http://www.ncbi.nlm.nih.gov
EMBL
http://www.ebi.ac.uk/
BLASTp or BLASTx
GenBank
http://www.ncbi.nlm.nih.gov
UniProt
Apweiler et al. (2004) and
Swiss-Prot
Boeckmann et al. (2003)
HMMER
Pfam
Bateman et al. (2004)
InterProscan a
InterPro
Mulder et al. (2003)
a InterPro itself is a metadatabase that provides access to commonly used signature
database such as Prosite, Prints, Pfam, ProDom, SMART, TIGR-fams, SCOP, Cath and
MSD see http://www.ebi.ac.uk/interpro/.
A. Meyerdierks and F.O. Glöckner
designed for metagenome analysis is currently being developed and will be available
at http://metagenomics.ics.nmpdr.org
2.4.5 Annotation Systems for Local Installation
The arguments for installing an annotation system locally are mainly an improved
flexibility in handling and visualizing the data (Gans and Wolinsky 2007). After
the first round of data mining using web-based annotation systems, users normally
ask for custom tailored views on their data. To deal with such demands, full access
to the databases and tools is required. Since the advent of genomics at the beginning of the 1990s several annotation systems have been made available for local
installation. The most prominent are MAGPIE (Gaasterland and Sensen 1996),
PEDANT Pro (Frishman et al. 2001), WIT/ERGO (Overbeek et al. 1999, 2000)
and ARTEMIS (Rutherford et al. 2000). Currently, one of the most advanced is the
recently developed GenDB system (Meyer et al. 2003) which has been adopted by
the Networks of Excellence “Marine Genomics Europe” as their standard platform
for data processing and annotation.
Without going into details about the pros and cons of the different annotation
systems (an overview can be found in Stothard and Wishart 2006), we would like
to suggest that the data model and versatility of GenDB is the most appropriate
for the emerging demands of metagenomics. Starting with gene prediction, several options can currently be chosen in GenDB: 1. to run single gene finders such
as Glimmer (Delcher et al. 2007), Critica (Badger and Olsen 1999) or 2. to use a
combination of two gene finders united in the tool Reganor (McHardy et al. 2004).
Exchanging the preconfigured gene predictors by MetaGene or combined systems
(Bauer et al. 2006) can be done easily using a local installation. The standard tools
and databases for providing functional observations for the predicted genes can be
found in Table 2.1. Information about the location of a protein can be procured by
Table 2.1 Standard tools and databases providing functional observations
Tool
Databases
References
BLASTn
GenBank
http://www.ncbi.nlm.nih.gov
EMBL
http://www.ebi.ac.uk/
BLASTp or BLASTx
GenBank
http://www.ncbi.nlm.nih.gov
UniProt
Apweiler et al. (2004) and
Swiss-Prot
Boeckmann et al. (2003)
HMMER
Pfam
Bateman et al. (2004)
InterProscan a
InterPro
Mulder et al. (2003)
a InterPro itself is a metadatabase that provides access to commonly used signature
database such as Prosite, Prints, Pfam, ProDom, SMART, TIGR-fams, SCOP, Cath and
MSD see http://www.ebi.ac.uk/interpro/.