genomic databases

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