Sonia Abdelhak Institut Pasteur Tunis Ahmed Rebaï Centre of Biotechnology Sfax Fredj Tekaia Institut Pasteur Paris Genomes Databases and Open Access Bibliographic Resources

Outline General introduction and overview of complete genome sequences Genomes databases and where to find them Comparative Genomics Databases Other Omics resources Bibliographic/Open access resources

Why databases? In the genomic era we have billions of data that need to be stored, curated and made accessible for analysis and knowledge discovery Databases are essential resources for both experimental and computational biologists We have crossed the Terabyte threshold of genomic data (Huge, massive, explosion!)

Chronology of completely sequenced genomes 1977: first viral genome (5386 base pairs; encoding 11 genes). Sanger et al. sequence bacteriophage  X : Human mitochondrial genome. 16,500 base pairs ( encodes 13 proteins, 2 rRNA, 22 tRNA ) 1986: Chloroplast genome. 156,000 base pairs (most are 120 kb to 200 kb)

1995: first genome of a free-living organism, the bacterium Haemophilus influenzae, by TIGR, 1830 Kb, 1713 genes. 1996: first genome of an archaeal genome: Methanococcus jannaschii DSM 2661, by TIGR, 1664 Kb, 1773 genes. 1997: first eukaryotic genome : Saccharomyces cerevisiae S288C; International collaboration; 16 Chromosomes; 12,057 Kb, ~6000 genes. 1998: first multicellular organism Nematode Caenorhabditis elegans; 97 Mb; ~19,000 genes.

1999: first human chromosome: Chromosome 22 (49 Mb, 673 genes))

2000: Fruitfly Drosophila melanogaster (137 Mb; ~13,000 genes) 2000 first plant genome: Arabidopsis thaliana (115,428 Mb; genes 2001: draft sequence of the human genome (3300 Mb; ~28000 genes) 2002: Plasmodium falciparum (22,9 Mb; 5334 genes) 2002: mouse genome (2700 Mb; ~28000 genes) 2004: Fish draft Tetraodon nigroviridis genome (x Mb; ~28000 genes); 2005: Dog (41Mb, genes) and chicken genomes ( genes)

Tree of life Complete genomes  2467 projects 524 published ( ) 1091 Bacteria 59 Archaea 720 eukaryotes 3 phylogenetic domains; Lifestyles: mesophiles; (hyper)thermophiles; psychrophiles;extreme conditions,...

Genome sequencing projects There are several web-based resources that document the progress of completely sequenced genomes and their reference publication, including: GOLDGenomes Online Database

How big are genome sizes? Viral genomes: 1 kb to 360 kb ( Canarypox virus) Note: Mimivirus: 1.2 Mb (Top 100 largest viral genome sequences) Bacterial genomes: 0.5 Mb to 13 Mb; Eukaryotic genomes: 8 Mb to 670 Gb; Database of Genome sizes:

Genome Sizes (MegaBases)

BIOLOGICAL DATABASE CATEGORIES Databases of nucleic acid sequences (RNA, DNA) Databases of protein sequences Databases of protein motifs and protein domains Databases of structures Databases of genomes Databases of genes Databases of expression profiles Databases of SNPs and mutations Databases of metabolic pathways and protein associations Databases of taxonomy …

Can we find a list of ‘clean’ databases ?

The NAR Database issue The 2007 update includes 968 databases, 110 more than the previous one. 68 new databases updates of 106 existing databases The complete database list and summaries are available online on the Nucleic Acids Research web site

NAR Database Category List Nucleotide Sequence Databases RNA sequence databases Protein sequence databases Structure Databases Genomics Databases (non-vertebrate) Metabolic and Signaling Pathways Human and other Vertebrate Genomes Human Genes and Diseases Microarray Data and other Gene Expression Databases Proteomics Resources Other Molecular Biology Databases Organelle databases Plant databases Immunological databases

Genomics Databases (non-vertebrate) –MGD - Mouse Genome Database ?????MGD - Mouse Genome Database –TIGR Gene Indices ?????TIGR Gene Indices –Genome annotation terms, ontologies and nomenclatureGenome annotation terms, ontologies and nomenclature –Taxonomy and identificationTaxonomy and identification –General genomics databasesGeneral genomics databases –Viral genome databasesViral genome databases –Prokaryotic genome databasesProkaryotic genome databases –Unicellular eukaryotes genome databasesUnicellular eukaryotes genome databases –Fungal genome databasesFungal genome databases –Invertebrate genome databasesInvertebrate genome databases

Three type of Genome database Databases which collect data of all sequenced genomes (Entrez_Genomes; EBI_genomes) Databases which collect data of a category of organisms with sequenced genomes (Microbial Genomes at TIGR) Databases specific for one organism with sequenced genomes (Flybase, MGD, Ensembl)

Genome databases contain genomic information collected from many sources. – Genome assembly – Gene predictions – Known genes, mRNA, ESTs, proteins – Genetic maps, markers and polymorphisms – Gene expression and phenotypes – Annotations – Interspecies homologues What kind of information you find there?

Resources for genomes There are two main resources for genomes: EBIEuropean Bioinformatics Institute NCBINational Center for Biotechnology Information But many others resources from sequencing Institutions: SangerThe welcome Trust Sanger Institute TIGRThe Institute for Genomic Research Genolevureshttp://cbi.labri.fr/Genolevures/index.phphttp://cbi.labri.fr/Genolevures/index.php

Eucaryotic genomes: Bacteria, fungi genomes: =11:Fungi|12: =11:Fungi|12 Insects: p=11:|12:Insects p=11:|12:Insects Plant genomes: Databases by phylogenetic groups

The (ever expanding) Entrez System Entrez PopSet Structure PubMed Books 3D Domains Taxonomy GEO/GDS UniGene Nucleotide Protein Genome OMIM CDD/CDART Journals SNP UniSTS PubMed Central

Mouse Assembly RefSeq Contig RefSeq Contig BAC WGS Other GenBank Other GenBank RefSeq Transcript RefSeq Transcript UniGene Transcript UniGene Transcript

Maps and Options

Common features of genomic database Possibility to download all the sequences of the genome or part of them (chromosomes, clones, genes, CDS,..) Most of them have a corresponding protein resource (the set of proteins obtained by translating all CDS) Example: Entrez-Genome of the NCBI Genpept

Comparative Genomics databases

Comparative genomics Analyses of the genetic material of different species help understanding the similarity and differences between genomes, their evolution and the evolution of their genes. Intra-genomic comparisons help understanding the degree of duplication (genome regions; genes) and genes organization,... Inter-genomic comparisons help understanding the degree of similarity between genomes; degree of conservation between genes; understanding gene and genome evolution

COGs: Clusters of Orthologous Groups: Internet resources for whole-genome comparative analysis and associated tools Resource URL UCSC Genome4 Bioinformaticshttp://genome.ucsc.edu/ Ensemblhttp:// MapViewerhttp:// VISTA Genome Browserhttp://pipeline.lbl.gov/ K-BROWSERhttp://hanuman.math.berkeley.edu/cgi-bin/kbrowser2 Comparative Regulatory Genomicshttp://corg.molgen.mpg.de/ GALAhttp:// EnsMarthttp:// ETOPEhttp:// PipMaker and MultiPipMakerhttp:// VISTA serverhttp://www-gsd.lbl.gov/vista/ MAVID serverhttp://baboon.math.berkeley.edu/mavid/ zPicture serverhttp://zpicture.dcode.org/ rVISTA serverhttp://rvista.dcode.org/

UCSC Comparative Genomics

NCBI Homo sapiens Genome: Statistics -- Build 36 version 2 Genes 28,961

Some considerations Organism specific databases can be more up-to-date than general databases Genome databases are not a one stop shop for all information, other databases like UniProt are still needed!

Bibliographic Databases and Open Access resources

Pubmed An access to more than 12 millions papers since 1950 (3790 jounals) Simple and advanced literature Search with keywords, author name, MESH terms, journals, single citation,.. Some papers are free from the journal website or through the editors

Pubmed central

Free access journals Authors pay to allow readers to get the papers free The BMC initiative The Plos initiative Other initiatives: some journals are giving immediate free online access and others after few (1-12) months from publication

Biomedcentral (BMC)

The PLOS initiative

Highwire

The HINARI initiative The Health InterNetwork Access to Research Initiative (HINARI) provides free or very low cost online access to the major journals in biomedical and related social sciences to local, not-for-profit institutions in developing countries. HINARI was launched in January 2002, with some 1500 journals from 6 major publishers. 22 additional publishers joined in May 2002, bringing the total number of journals to over Today more than 70 publishers are offering their content in HINARI and others will soon be joining the programme.

And also books!

If you want to learn Just try and RTM

General genomics databases –Animal Genome Size DatabaseAnimal Genome Size Database –BacMapBacMap –COG - Clusters of Orthologous Groups of proteinsCOG - Clusters of Orthologous Groups of proteins –CoGenT++CoGenT++ –DEG - Database of Essential GenesDEG - Database of Essential Genes –EBI GenomesEBI Genomes –Entrez GeneEntrez Gene –Entrez GenomesEntrez Genomes –ERGO-LightERGO-Light –GenDiSGenDiS –GeneNestGeneNest –Genome information brokerGenome information broker –Genome Project DatabaseGenome Project Database –Genome ReviewsGenome Reviews –GOLDGOLD –GtRDB - Genomic tRNA DatabaseGtRDB - Genomic tRNA Database –InparanoidInparanoid –Integr8 (formerly Proteome Analysis Database)Integr8 (formerly Proteome Analysis Database) –INVHOGENINVHOGEN –KaryotypeDBKaryotypeDB –KEGG - Kyoto Encyclopedia of Genes and GenomesKEGG - Kyoto Encyclopedia of Genes and Genomes –MBGD - Microbial Genome DatabaseMBGD - Microbial Genome Database –MeGXMeGX –MetaCycMetaCyc –NegProt - Negative Proteome databaseNegProt - Negative Proteome database