This document discusses genomic databases. It begins by defining key terms like genes, genomes, and genomics. It then describes categories of biological databases including those for nucleic acid sequences, proteins, structures, and genomes. It provides many examples of genomic databases for both non-vertebrate and vertebrate species, including databases for bacteria, fungi, plants, invertebrates, and humans. The final sections note that genomic databases collect genome-wide data from various sources and that databases can be specific to a single organism or category of organisms.

1. GENOMIC DATABASES
DR SATYABRATA SAHOO
2nd 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.

5. 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.

6. 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.

8. CONT..

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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.

15. 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

16. 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

17. 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

18. 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)

27. MOUSE ASSEMBLY

31. 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.

32. THANK U