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Overview of Microbial Pathway and Genome Databases

Explore various online resources that integrate microbial genomes and pathway information. This detailed overview compares databases, genomes included, computational processing applied, query tools, visualization features, and more.

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Overview of Microbial Pathway and Genome Databases

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  1. Overview of Microbial Pathway and Genome Databases

  2. Overview • Survey of other databases / web sites that integrate hundreds of microbial genomes and pathway information • Most of these resources are described in publications that can be found via PubMed • Differences among each resource include: • Genomes included • What other information is integrated with the genome data • Value-added computational processing applied to each genome • Query, visualization, and analysis tools available at each site

  3. Overall Comparison to BioCyc • Many of the other databases contain more genomes than BioCyc • This will change in 2011 as BioCyc transitions to RefSeq as its genome source • BioCyc Tier 1 and Tier 2 databases more highly curated than other databases • BioCyc has more extensive query, visualization, and analysis tools than other sites • BioCyc desktop version can be installed locally, and allows editing of PGDBs • Some other sites re-annotate the genomes, which may or may not improve data quality

  4. Microbial Genome Resources • CMR – Comprehensive Microbial Resource • Entrez • IMG – Integrated Microbial Genomes • KEGG – Kyoto Encyclopedia of Genes and Genomes • PATRIC • SEED/NMPDR • UMBBD – Univ of Minnesota Biocatalysis Biodegradation Database

  5. CMR – Comprehensive Microbial ResourceJ. Craig Venter Institute • http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi • ~700 genomes • Genome data only, no pathways • Genome browser, gene pages • Many comparative operations • Will be discontinued later in 2010

  6. Entrez GenomesNational Center for Biotechnology Information • http://www.ncbi.nlm.nih.gov/sites/genome • Web portal to Genbank genomes • Genome browser, gene pages

  7. IMG – Integrated Microbial GenomesJoint Genome Institute • http://img.jgi.doe.gov/cgi-bin/pub/main.cgi • 1,911 microbial genomes (approx half are draft quality) • Genome browser, gene pages • Many comparative operations • Genome context analyses available

  8. PATRICVirginia Bioinformatics Institute • http://patric.vbi.vt.edu/ • Genome browser, gene pages • KEGG pathways

  9. SEED / NMPDRArgonne National Laboratory • http://www.nmpdr.org/FIG/wiki/view.cgi • 782 microbial genomes • Funding ended in 2009 • Unique features: • Systems • Essential genes • Comparative genomics tools • Community annotation

  10. UMBBDUniversity of Minnesota • http://umbbd.msi.umn.edu/ • Database of ~150 microbial biodegradation pathways • Does not include full microbial genomes

  11. KEGG – Kyoto Encyclopedia of Genes and GenomesKyoto University • http://www.genome.ad.jp/kegg/ • 1,382 organisms • KEGG reannotates each genome • Static reference pathway maps are colored with the genes present in each organism

  12. Comparison with KEGG • KEGG vs MetaCyc: Reference pathway collections • KEGG maps are not pathways Nuc Acids Res 34:3687 2006 • KEGG maps contain multiple biological pathways • Two genes chosen at random from a BioCyc pathway are more likely to be related according to genome context methods than from a KEGG pathway • KEGG maps are composites of pathways in many organisms -- do not identify what specific pathways elucidated in what organisms • KEGG has no literature citations, no comments, less enzyme detail • KEGG assigns half as many reactions to pathways as MetaCyc • KEGG vs organism-specific PGDBs • KEGG does not curate or customize pathway networks for each organism • Highly curated PGDBs now exist for important organisms such as E. coli, yeast, mouse, Arabidopsis

  13. Comparison of Pathway Tools to KEGG • Inference tools • KEGG does not predict presence or absence of pathways • KEGG lacks pathway hole filler, operon predictor • Curation tools • KEGG does not distribute curation tools • No ability to customize pathways to the organism • Pathway Tools schema much more comprehensive • Visualization and analysis • KEGG does not perform automatic pathway layout • KEGG metabolic-map diagram extremely limited • No comparative pathway analysis

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