Part B | 11.3
314 Part B Tools and Methods in Marine Biotechnology
Table 11.2 Websites of initiatives of genomic and metagenomic data generation, repository and/or analysis tools, useful for marine
microbial bioprospecting
Initiative/Website
Description
Genomic Encyclopedia of Bacteria and Archaea (GEBA)
project
www.jgi.doe.gov/programs/GEBA
It aims at systematically filling in the gaps in sequencing
along the bacterial and archaeal branches of the tree of
life
Marine Microbial Genome Sequencing Project
http://camera.calit2.net/microgenome
Its aim is to increase the number of whole genome sequences of ecologically relevant marine microorganisms
Genomes Online Database (GOLD)
www.genomesonline.org/cgi-bin/GOLD/index.cgi
Resource for comprehensive access to information regarding genome and metagenome sequencing projects,
and their associated metadata
Integrated Microbial Genomes and Metagenomes System
(IMG and IMG/M)
http://img.jgi.doe.gov
Community resource for analysis and annotation of
genome and metagenome datasets in a comprehensive
comparative context
National Center for Biotechnology Information (NCBI)
Genome and Sequence Read Archive (SRA)
www.ncbi.nlm.nih.gov
NCBI Genome organizes information on genomes including sequences, maps, chromosomes, assemblies, and
annotations. The NCBI SRA stores raw sequencing data
from the next generation of sequencing platforms
Metagenomics Analysis Server (MG-RAST)
http://metagenomics.anl.gov
The MG-RAST server is an automated analysis platform
for metagenomes providing quantitative insights into microbial populations based on sequence data
Microbial Ecological Genomics DataBase (MegDB)
www.megx.net
MegDB is a collection of publicly available georeferenced marine bacterial and archaeal genomes and
metagenomes
Earth Microbiome Project (EMP)
www.earthmicrobiome.org
Massive multidisciplinary effort to analyze microbial
communities across the globe, using metagenomics,
metatranscriptomics, and amplicon sequencing
Microme
www.microme.eu
Resource for bacterial metabolism, whose aim is to support the large scale inference of metabolic flux directly
from genome sequence
Microbial Genome Annotation & Analysis Platform (MicroScope)
www.genoscope.cns.fr/agc/microscope/home/index.php
Web-based platform for microbial comparative genome
analysis and manual functional annotation
Text Mining for Bacterial Enzymes (TeBactEn)
http://tebacten.bioinfo.cnio.es
Tool designed to facilitate the retrieval, extraction and
annotation of bacterial enzymatic reactions and pathways
from the literature
Characterized Protein Database (CharProtDB)
www.jcvi.org/charprotdb/index.cgi/home
Resource of expertly curated, experimentally characterized proteins described in published literature
Natural Product Domain Seeker (NaPDoS)
http://napdos.ucsd.edu
Bioinformatic tool for the rapid detection and analysis of
secondary metabolite genes
MetaBioME: A Comprehensive Metagenomic BioMining
Engine
http://metasystems.riken.jp/metabiome
Web resource to find novel homologs for known commercially useful enzymes in metagenomic datasets and
completed bacterial genomes
tative sequences [11.85]. This bias has a negative effect
on gene discovery and annotation in both genomic and
metagenomic data, as microbial genomes provide scaffolds for the interpretation of sequence information.
With the aim of systematically filling in these existing gaps, the US Department of Energy’s Joint Genome
314 Part B Tools and Methods in Marine Biotechnology
Table 11.2 Websites of initiatives of genomic and metagenomic data generation, repository and/or analysis tools, useful for marine
microbial bioprospecting
Initiative/Website
Description
Genomic Encyclopedia of Bacteria and Archaea (GEBA)
project
www.jgi.doe.gov/programs/GEBA
It aims at systematically filling in the gaps in sequencing
along the bacterial and archaeal branches of the tree of
life
Marine Microbial Genome Sequencing Project
http://camera.calit2.net/microgenome
Its aim is to increase the number of whole genome sequences of ecologically relevant marine microorganisms
Genomes Online Database (GOLD)
www.genomesonline.org/cgi-bin/GOLD/index.cgi
Resource for comprehensive access to information regarding genome and metagenome sequencing projects,
and their associated metadata
Integrated Microbial Genomes and Metagenomes System
(IMG and IMG/M)
http://img.jgi.doe.gov
Community resource for analysis and annotation of
genome and metagenome datasets in a comprehensive
comparative context
National Center for Biotechnology Information (NCBI)
Genome and Sequence Read Archive (SRA)
www.ncbi.nlm.nih.gov
NCBI Genome organizes information on genomes including sequences, maps, chromosomes, assemblies, and
annotations. The NCBI SRA stores raw sequencing data
from the next generation of sequencing platforms
Metagenomics Analysis Server (MG-RAST)
http://metagenomics.anl.gov
The MG-RAST server is an automated analysis platform
for metagenomes providing quantitative insights into microbial populations based on sequence data
Microbial Ecological Genomics DataBase (MegDB)
www.megx.net
MegDB is a collection of publicly available georeferenced marine bacterial and archaeal genomes and
metagenomes
Earth Microbiome Project (EMP)
www.earthmicrobiome.org
Massive multidisciplinary effort to analyze microbial
communities across the globe, using metagenomics,
metatranscriptomics, and amplicon sequencing
Microme
www.microme.eu
Resource for bacterial metabolism, whose aim is to support the large scale inference of metabolic flux directly
from genome sequence
Microbial Genome Annotation & Analysis Platform (MicroScope)
www.genoscope.cns.fr/agc/microscope/home/index.php
Web-based platform for microbial comparative genome
analysis and manual functional annotation
Text Mining for Bacterial Enzymes (TeBactEn)
http://tebacten.bioinfo.cnio.es
Tool designed to facilitate the retrieval, extraction and
annotation of bacterial enzymatic reactions and pathways
from the literature
Characterized Protein Database (CharProtDB)
www.jcvi.org/charprotdb/index.cgi/home
Resource of expertly curated, experimentally characterized proteins described in published literature
Natural Product Domain Seeker (NaPDoS)
http://napdos.ucsd.edu
Bioinformatic tool for the rapid detection and analysis of
secondary metabolite genes
MetaBioME: A Comprehensive Metagenomic BioMining
Engine
http://metasystems.riken.jp/metabiome
Web resource to find novel homologs for known commercially useful enzymes in metagenomic datasets and
completed bacterial genomes
tative sequences [11.85]. This bias has a negative effect
on gene discovery and annotation in both genomic and
metagenomic data, as microbial genomes provide scaffolds for the interpretation of sequence information.
With the aim of systematically filling in these existing gaps, the US Department of Energy’s Joint Genome