Genomic databases
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The document discusses various types of biological databases, focusing on genomic databases that serve as repositories for raw data from DNA and protein sequences. Key examples include GenBank, EMBL, SGD, and UniGene, each providing specific functionalities for sequence data retrieval and analysis. The document highlights the collaborative nature of these databases and their role in facilitating genomic research and evolutionary studies.
Genomic databases
- 1. Types of Biological Databases Genomic Databases Amandeep Singh Assistant Professor Department of Biotechnology GSSDGS Khalsa College Patiala
- 2. Primary Database It act as repository of raw data (came directly through experimentation) For DNA (Nucleotide/Genome Sequence Database) For Protein (Proteome Sequence Database) 1. GenBank 2. EMBLE 1. SWISS-PROT 2. PIR
- 3. Nucleotide and Genome Sequence Database GenBank • NIH genetic sequence database. • Annotated collection of all publically available DNA sequences. • A new release is made every two months. GenBank International Nucleotide Sequence Database Collaboration DNA Data Bank of Japan European Molecular Biology Laboratory (EMBL) National Center for Biotechnology Information (NCBI)
- 4. GenBank Entry 1. Concise description of sequence 2. Scientific nomenclature and taxonomy of source organism 3. Table of features:- Coding region and sites • Transcription site • Mutation site • Modification site 4. Protein translation of coding region 5. Bibliographic references
- 5. EMBLE (European Molecular Biology Laboratory) Nucleotide Sequence Database maintained by European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. Accessed Through SRS System (Sequence Retrieval System) At EBI Download entire database as single flat file
- 6. UniGene GenBank Sequence Non-redundant Gene Cluster Represent a Unique Gene ATGCATGCATGC ATGCATGCATGC ATGCATGCATGCAT ATGCATGCATGCATGC ATGCATGCATGCATGCAT
- 7. SGD (Saccharomyces Genome Database) About molecular biology and genetics of yeast Saccharomyces Cerevisiae
- 8. EBI Genome Provide access and statistic for complete genomes and information about ongoing projects.
- 9. Ensemble • Joint Project between EMBL-EBI + Sanger Center • To develop software system that produce and maintain automatic annotation on eukaryotic genomes.
- 10. Entrez Retrieval system for searching several linked databases.
- 11. Gene Census • Provide entry point for genome analysis with an interactive whole genome comparison from an evolutionary perspective. • Build Phylogenetic trees
- 12. COGs • This database classify proteins encoded in 43 complete genomes on the basis of sequence similarity. • Cluster of Orthologous Group (COGs): A collection of homologous genes that are useful for study of evolutionary relationships. • Basic application:- Predict the function of uncharacterized protein to characterized protein and to identify phylogenetic patterns of protein occurrence.