Genomes Databases and Open Access Bibliographic Resources

Sonia Abdelhak Institut Pasteur Tunis Ahmed Rebaï Centre of Biotechnology Sfax Fredj Tekaia Institut Pasteur Paris

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

f

X174.

• 1981: Human mitochondrial genome . 16,500 base pairs ( encodes 13 proteins, 2 rRNA, 22 tRNA ) • 1986: Chloroplast genome.

(most are 120 kb to 200 kb) 156,000 base pairs

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 Mb; 22670 genes • 2001: first plant genome: Arabidopsis thaliana (115,428 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

~28000 genes); genome (x Mb; • 2005 : Dog (41Mb, 33651 genes) and chicken genomes ( 18031 genes)

Tree of life

http://www.genomesonline.org/

Complete genomes



2467 projects • 524 published (03-17-07) • 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: GOLD Genomes Online Database http://www.genomesonline.org/gold.cgi

How big are genome sizes?

Viral genomes: 1 kb to 360 kb ( Canarypox virus) Note: Mimivirus: 1.2 Mb

http://www.giantvirus.org/top.html

(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:

http://www.cbs.dtu.dk/databases/DOGS/index.php

Genome Sizes (MegaBases)

3500 3000 2500 2000 1500 1000 500 0 E.coli

Yeast Worm Fly 600000 500000 Fugu Human 400000 300000 Size 200000 100000 0 Fly Fugu Human Wheat Amoeba Size

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 http://nar.oxfordjournals.org/

• • • • • • • • • • • • • •

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 ?????

TIGR Gene Indices ?????

Genome annotation terms, ontologies and nomenclature Taxonomy and identification General genomics databases Viral genome databases Prokaryotic genome databases Unicellular eukaryotes genome databases Fungal genome databases Invertebrate 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)

What kind of information you find there?

• 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

Resources for genomes There are two main resources for genomes: EBI European Bioinformatics Institute http://www.ebi.ac.uk/genomes/ NCBI National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/Genomes/ But many others resources from sequencing Institutions: Sanger The welcome Trust Sanger Institute

http://www.sanger.ac.uk/

TIGR Genolevures The Institute for Genomic Research http://cmr.tigr.org/tigr-scripts/CMR/shared/Genomes.cgi

http://cbi.labri.fr/Genolevures/index.php

Databases by phylogenetic groups

Eucaryotic genomes: http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi

Bacteria, fungi genomes =11:Fungi|12 : : http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi?p3=11:Fungi&taxgroup Insects: http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi?p3=12:Insects&taxgrou p=11:|12:Insects Plant genomes: http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html

...

The

(ever expanding)

Entrez System

3D Domains Structure CDD/CDART Protein OMIM PubMed PubMed Central Journals Books Entrez Taxonomy GEO/GDS UniGene Nucleotide SNP Genome UniSTS PopSet

RefSeq Contig BAC WGS Other GenBank UniGene Transcript

Mouse Assembly

RefSeq 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

Internet resources for whole-genome comparative Resource analysis and associated tools URL

UCSC Genome4 Bioinformatics Ensembl http://genome.ucsc.edu/ http://www.ensembl.org/ MapViewer http://www.ncbi.nlm.nih.gov/mapview/ VISTA Genome Browser K-BROWSER http://pipeline.lbl.gov/ http://hanuman.math.berkeley.edu/cgi-bin/kbrowser2 Comparative Regulatory Genomics GALA http://www.bx.psu.edu/ http://corg.molgen.mpg.de/ EnsMart http://www.ensembl.org/EnsMart/ ETOPE http://www.bx.psu.edu/ PipMaker and MultiPipMaker VISTA server http://www.bx.psu.edu/ http://www-gsd.lbl.gov/vista/ MAVID server zPicture server rVISTA server http://baboon.math.berkeley.edu/mavid/ http://zpicture.dcode.org/ http://rvista.dcode.org/ COGs: Clusters of Orthologous Groups: http://www.ncbi.nlm.nih.gov/COG/

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 http://www.pubmed.org/

• 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 http://www.pubmedcenral.com/

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) http://www.biomedcentral.com/

The PLOS initiative http://www.plos.org/

Highwire http://highwire.stanford.edu/

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 2000. • 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 Database – – – – – – – – – – – – – – – – – – – – – – – – BacMap COG - Clusters of Orthologous Groups of proteins CoGenT++ DEG - Database of Essential Genes EBI Genomes Entrez Gene Entrez Genomes ERGO-Light GenDiS GeneNest Genome information broker Genome Project Database Genome Reviews GOLD GtRDB - Genomic tRNA Database Inparanoid Integr8 (formerly Proteome Analysis Database) INVHOGEN KaryotypeDB KEGG - Kyoto Encyclopedia of Genes and Genomes MBGD - Microbial Genome Database MeGX MetaCyc NegProt - Negative Proteome database