Dna – rna protein Functional genomics

DNA – RNA - Protein

Functional genomics

Genomics: from sequence to predicted function

Microbial genomes

• Microbial genome sequencing

• 1995-2000: Mainly pathogenic bacteria

Biological Databases

• Database types:

• sequence EMBL, GenBank

• annotation SwissProt

• enzyme Enzyme, Brenda

• genome Entrez, EBI-Genome Reviews

• structure PDB, SCOP

• pathway KEGG, EcoCyc

• organism FlyBase, WormBase

• organizational Pfam, COG

• Summarized each year in Nucleic Acids Res., January issue

Genome Databases

• Main databases

• NCBI Entrez

• www.ncbi.nlm.nih.gov/genomes/lproks.cgi

• EBI Genome Reviews

• www.ebi.ac.uk/genomes/bacteria.html

• TIGR Comprehensive Microbial Resource (CMR)

• www.tigr.org/tdb

• Integrated Genomics GOLD

• www.genomesonline.org

• CBS Genome Altas

• www.cbs.dtu.dk/services/GenomeAtlas

Genome Databases

• Specialized databases

• Sanger Institute own genomes, many pathogenic bacteria

• (UK) www.sanger.ac.uk/projects

• Pasteur Institute own genomes, many pathogenic bacteria

• (France) www.pasteur.fr/english.html

• MIPS PEDANT – all genomes

• (Germany) http://pedant.gsf.de/

• DOE-JGI own genomes, many microbial - environmental

• (USA) http://genome.jgi-psf.org/microbial/

Genome Databases

• Overviews of databases

• ABIM organism databases

• (France) www.up.univ-mrs.fr/~wabim/english/genome.html

• Complete Genomes

• COGENT (COmplete GENome Tracking : a flexible data environment for computational genomics) EBI (UK)

• Complete genomes NCBI (Haemophilius influenza, E. Coli, Mycoplasma genitalium)

• Completed Genomes at the EBI EBI (UK)

• Completed microbial genomes InfoBioGen (France)

• Completed microbial genomes TIGR

• Completely sequenced genomes Rockfeller (USA)

• EMGLib (completely sequenced bacterial genomes and the yeast genome) PBIL (France)

• Fully Sequenced Genomes Present In The Public DataBases GOLD (USA)

• Integr8 (integrated views of complete genomes and proteomes) EBI (UK)

• PEDANT (Protein Extraction, Description, and Analysis Tool) MIPS (more 200 genomes) (Germany)

• E. Coli : Wisconsin (USA), see also Entrez (NCBI)

• Rfam (annotating non-coding RNAs in complete genomes) Saint Louis (USA), see also Sanger (UK)

• SACSO (Systematic Analysis of Completely Sequenced Organisms) Pasteur (French)

• TIGR : Genomes (USA)

• Yeast Genome Project (Complete genome) MIPS (Germany), see also Genome Viewer, see also Comprehensive Yeast Genome Database

Genome Databases

• Comparative genomics databases

• ERGO Comparative genomics analysis

• (USA) http://ergo.integratedgenomics.com/ERGO

Genome Databases

• Comparative genomics databases

• STRING Search Tool for the Retrieval of Interacting Genes/Proteins

• (De) http://www.bork.embl-heidelberg.de/STRING

Genome Databases

• Metabolic pathway-genome databases (PGDB)

• KEGG Kyoto Encyclopedia of Genes and Genomes

• (Japan) http://www.genome.jp/kegg/kegg2.html

• EcoCyc E.coli metabolic pathways

• (highly curated)

• (USA) http://www.ecocyc.org.

• BioCyc collection of PGDBs

• http://www.biocyc.org