The document discusses various types of biological databases including nucleotide databases, genomic databases, protein databases, and metabolic databases. It provides examples of several specific databases, such as Nucleotide databases like GenBank, genomic databases like Entrez Genome, protein databases like UniProt, and metabolic databases like KEGG. It also discusses the different levels of data in biological databases from primary data directly from experiments to secondary data that is analyzed and derived from primary data.

1. Biological Databases Shweta Kagliwal

2. Units of biological information Database Types Look at some databases Synopsis

3. Data Primary or derived data: Primary databases: direct experimental results Secondary databases: result of analysis on primary databases Sequences Structure Genome Pathways Lipids, Carbohydrates Literature

4. Crop Information Systems Taxonomic Databases Nucleotide Databases Genomic Databases Protein Databases Metabolic Pathway Databases Bibliographic Databases Data Levels Primary Secondary Primary Databases Secondary databases Database Types General plant/animal genera specific Organism specific Public Commercial Subject wise Taxonomy wise Ownership wise

5. Taxonomic Databases TaxBrowser GRIN Taxonomy for Plants Species 2000

6. The nucleotide sequence databases are data repositories, accepting nucleic acid sequence data from the scientific community and making it freely available. Nucleotide Databases

7. A Sample Record

8. Specialized Nucleotide Databases Focussing on particular feature 1) Markers 2) Mitop2 – organelle specific 3) HIV-SD 4) REBASE - for restriction enzymes & restriction enzyme sites.

9. Bibliographic/Literature Databases Scientific literature databases have been available since the 1960’s. Pubmed OMIM/OMIA AGRICOLA

10. In addition to the human genome, the genomes of about 800 organisms have been sequenced in recent years. Entrez Genome -- A resource from the National Center for Biotechnology Information (NCBI) for accessing information about completed and in-progress genomes. ( PGDIC ) The 'Plant Genome Information Resource' provides access to many different plant genome databases, including chlamydomonas, cotton, alfalfa, wheat, barley, rye, rice, millet, sorghum and species of solanaceae and trees. Genomic Databases

11. Prokaryotes Completed Draft In Progress Archae 67 13 41 Bacteria 912 1085 1099 Eukaryotes Animals 4 79 56 Plants 2 14 45 Fungi 10 77 38 Protists 6 24 24 Revised: Dec 11, 2009 Complete & Ongoing Genomic Projects

12. Plant Sequencing Projects

13. Protein Databases Primary protein sequence databases such as UniProt/SwissProt Structure databases such as PDB Specialized protein databases such as ENZYME

14. Metabolic Databases KEGG Pathway Database Ecocyc AraCyc, RiceCyc, SorghumCyc, LycoCyc, CapCyc, etc.

15. AraCyc Statistics

16. Compound Pathway Gene Enzyme Reaction

17. Secondary Databases Pfam ( pfam.sanger.ac.uk/ ) Pfam is a database of protein families defined as domains (contiguous segments of entire protein sequences). For each domain, it contains a multiple alignment of a set of defining sequences (the seeds) and the other sequences in SWISS-PROT and TrEMBL that can be matched to that alignment . PROSITE ( www.expasy.ch/prosite/) PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. InterPro InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites