Genomic databases

genomic databases

1. GENOMIC DATABASES DR SATYABRATA SAHOO 2 nd YR PGT DEPARTMENT OF PHARMACOLOGY SCB MCH ,CUTTACK

2. INTRODUCTION GENE - Functional unit regulated by transcription and encodes an RNA product which is most commonly, but not always, translated in to a protein that exerts activity within or outside cell. GENOME - Complete set of genes or genetic material present in a cell or organism . GENOMIC - An organism's entire genetic information, the genome and the function and interaction of DNA within the genome .

3. Cont.. PHARMACOGENOMICS -The study of the role of the  genome in drug  response . BIOLOGICAL DATABASES - Libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.

4. BIOLOGICAL DATA BASE CATEGORIES Databases of nucleic acid sequences(RNA,DNA) Databases of protein sequences Databases of protein motifs and protein domains Databases of structures Databases of genome Databases of genes Databases of SNPs & mutations etc.

5. GENOMIC DATABASES GENOMIC DATABASES -  The official central repository for genomic mapping data resulting from the Human Genome. HUMAN GENOME PROJECT was initiated in the mid- 1980s. BIOINFORMATICS led to completion of a draft human sequence in 2000 and completion of DNA sequence for last of the human chromosomes in May 2006 . HUMAN DNA consists of 3 billion base pairs of DNA per haploid genome, which is nearly 1000 fold > Escherichia coli genome.

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7. Cont.. Genome databases contain genomic information collected from many sources. Genome assembly Gene predictions Known genes, mRNA , proteins Genetic maps, markers and polymorphisms Gene expression and phenotypes Annotations Interspecies homologues

8. GENOMIC DATABASES (NON VERTEBRATES ) AspGD Aspergillus  Genome Database BeetleBase  the model organism database for   Tribolium castaneum Cacao Genome Database Caenorhabditis  Genome Sequencing Projects Candida  Genome Database ChlamydDB  database for the green alga   Chlamydomonas reinhardtii  and related species The Cotton Genome Database Dendrome  A Forest Tree Genome Database EcoGene  the Database of  Escherichia coli  Sequence and Function Ensembl Genomes

9. CONT.. FlyBase  a database of the  Drosophila  genome GenProtEC   E.Coli  genome and proteome database GOBASE  the Organelle Genome Database Gramene  a resource for comparative grass genomics HGD  Hymenoptera Genome Database IGGI  International Glossina Genome Initiative PomBase     a scientific resource for fission yeast

10. CONT.. SGD   Saccharomyces  Genome Database SpBase   Strongylocentrotus purpuratus  Sea Urchin Genome Database StellaBase   Nematostella vectensis  Genomics Database TAIR  The Arabidopsis Information Resource VectorBase  invertebrate vectors of human pathogens WormBase  the biology and genome of  C. elegans

11. GENOMIC DATABASES OF VERTEBRATES AgBase   a curated , open-source resource for functional analysis of agricultural plant and animal gene products ARKdb  species databases includes: Cat, Chicken, Cow, Deer, Horse, Pig, Salmon, Sheep, Tilapia, Turkey BirdBase  A Database of Avian Genes and Genomes Bovmap  mapping the Bovine genome Chicken Genome Resources The Dog Genome Project

12. CONT.. Ensembl  genome databases for vertebrates and other eukaryotic species. Entrez Gene  searchable database of genes, from  RefSeq  genomes, defined by sequence and/or located in the  NCBI Map Viewer . Fugu  the Fugu genomics project Horse Genome Project Kangaroo Genome Project lizardbase  a centralized and consolidated informatics resource for lizard reseach .

13. CONT.. MGI  Mouse Genome Informatics National Animal Genome Research Program Pig Genome Coordination Program Porcine Genome Sequencing Project Pig Genome Resources Rabbit Genome Resources RGD   Rat Genome Database

14. HUMAN GENOMIC DATABASES Database of Genomic Variants dbVar  Database of Genomic Structural Variation ENCODE Project   ENCyclopedia Of DNA Elements Ensembl Human   human genes generated automatically by the Ensembl gene builder Entrez Gene  searchable database of genes, defined by sequence and/or located in the  NCBI Map Viewer Genome Reference Consortium  Putting sequences into a chromosome context

15. CONT.. GWAS Central  centralized compilation of summary level findings from genetic association studies HapMap  international HapMap Project H-Invitational Database  an integrated database of human genes and transcripts Human Genome Segmental Duplication Database Human Structural Variation Database 1000 Genomes  A Deep Catalog of Human Genetic Variation UCSC Human Genome Browser Gateway VEGA Human  manual annotation of finished genome sequence

16. TYPES OF GENOMIC 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 )

17. MOUSE ASSEMBLY

18. GENERAL CONSIDERATIONS Organism specific Databases can be more up-to- date than General Databases. Genomic Databases are not a one stop shop for all informations,other Databases like Uniport are still needed.

19. THANK U