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Genomes Databases and Open Access Bibliographic Resources

Genomes Databases and Open Access Bibliographic Resources. Antonio Basílio de Miranda Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz Fundação Oswaldo Cruz Rio de Janeiro - Brazil. Outline General introduction and overview of complete genome sequences

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Genomes Databases and Open Access Bibliographic Resources

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  1. Genomes Databases and Open Access Bibliographic Resources Antonio Basílio de Miranda Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz Fundação Oswaldo Cruz Rio de Janeiro - Brazil

  2. 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

  3. Why use 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.

  4. And what is a database system? • From Oxford Dictionary: • Database: an organized body of related information. • Database system, DataBase Management System (DBMS): a software system that facilitates the creation, maintenance and use of an electronic database.

  5. Common database models: HierarchicalNetworkRelationalObject-relationalObject Other models: AssociativeConcept-oriented Entity-Attribute-ValueMulti-dimensional Semantic data model Semi-structuredStar schemaXML database

  6. What is stored: • Nucleotide sequences • Protein sequences • Genomes • Patterns • Structures • Etc.

  7. Some problems: • Different data formats and technologies • Different types of data • Size • Redundancy • “Hereditary” mistakes • Inconsistent annotations

  8. Different formats – C. trachomatis pyruvate kinase

  9. Completely sequenced genomes – a timeline • 1977 first viral genome (5386 base pairs; encoding 11 genes). Sanger et al. sequence bacteriophage fX174. • 1981 Human mitochondrial genome. 16,500 base pairs (encodes 13 proteins, 2 rRNA, 22 tRNA). • 1986Chloroplast 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.

  10. 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). • 2000FruitflyDrosophila melanogaster (137 Mb; ~13,000 genes).

  11. 2000 first plant genome: Arabidopsis thaliana (115,428 Mb; 22670 genes • 2001 draft sequence of the human genome (3300 Mb; ~28000 genes) • 2002Plasmodium falciparum (22,9 Mb; 5334 genes) • 2002mouse genome (2700 Mb; ~28000 genes) • 2004Fish draft Tetraodon nigroviridis genome (x Mb; ~28000 genes); • 2005Dog (41Mb, 33651 genes) and chicken genomes ( 18031 genes)

  12. 2007James Watson’s genome is sequenced. • 2007Craig Venter publishes the results of his own sequenced genome. • October 2013Deadline for the X Prize Foundation challenge to sequence 100 human genomes for less than $10,000 each.

  13. www.genomesonline.org 3825 projects • 827 published (06-29-08) • 1842 bacteria • 90 archaea • 936 eukaryotes • 130 metagenomes

  14. Genome sequencing projects There are several web-based resources that document the progress of completely sequenced genomes and their reference publications, including: GOLD - Genomes Online Database http://www.genomesonline.org/gold.cgi

  15. 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

  16. Genome size and database increase

  17. 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 • •…

  18. Can we find a list of ‘clean’ databases ?

  19. The NAR database issue The 2008 update includes 1078 databases, 110 more than the previous one. 98 new databases updates of 84 existing databases 25 obsolete databases removed! The complete database list and summaries are available online on the Nucleic Acids Research web site http://nar.oxfordjournals.org/

  20. NAR database category list Nucleotide Sequence Databases RNA sequence databases Protein sequence databases Structure Databases Genomics Databases (non-vertebrate) Metabolic and Signalling 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

  21. 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

  22. Three types of genome databases: 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)

  23. 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

  24. 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 The Institute for Genomic Research http://cmr.tigr.org/tigr-scripts/CMR/shared/Genomes.cgi Genolevures http://cbi.labri.fr/Genolevures/index.php

  25. Databases by phylogenetic groups Eucaryotic genomes: http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi Bacteria, fungi genomes: http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi?p3=11:Fungi&taxgroup=11:Fungi|12: Insects:http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi?p3=12:Insects&taxgroup=11:|12:Insects Plant genomes:http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html ...

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

  27. Other GenBank WGS UniGene Transcript RefSeq Contig BAC RefSeq Transcript Mouse assembly

  28. Maps and Options

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