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Data retrieval

Biological data is widely distributed over the web and can be retrieved using search engines like Google or data retrieval tools. Dedicated data retrieval tools for molecular biologists include Entrez, DBGET, and SRS which allow text searching of linked databases and sequence searching. Entrez, developed by NCBI, integrates information from databases including GenBank, PubMed, and OMIM. DBGET covers databases like GenBank, EMBL, and PDB. SRS, developed by EBI, integrates over 80 molecular biology databases.

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Data Retrieval
Access to Distributed data Biological data is widely distributed over the WWW. Data can be retrieved by, 1. Search engines 2. Data retrieval tools
Search Engines Examples for Search Engines, Google Yahoo! Search LeapFish Bing Using Search engines 1. Can find relevant web pages 2. It is difficult to find desired information 3. Difficult to find specific information.
Leapfish
bing
Data retrieval tools Dedicated to access information for molecular biologists. Most widely used are, 1. Entrez 2. DBGET 3. SRS Each of these allows, - Text based searching of a no. of linked DBs. - Sequence searching. They differ in, - The DBs they cover - How the retrieved information is accessed and presented.
Entrez - WWW-based data retrieval system. - Developed by NCBI (National Centre for Biotechnology Information). - Integrates information held in different DBs.
Entrez Data bases covered by Entrez are, Nucleic acid - GenBank, RefSeq, PDB. Protein seqs - SWISS-PROT, PIR. 3D structures – MMDB Genomes – Many sources PopSet – From GenBank OMIM – OMIM Taxonomy – NCBI taxonomy database Books- Bookshelf ProbeSet – GEO (Gene Expression Omnibus) Literature - PubMed
Entrez
Entrez
DBGET An integrated data retrieval system developed and maintained by, - The Institute for Chemical Research (Kyoto University) - The Human Genome Center (University of Tokyo) Data bases covered are, Nucleic acid Seqs – GenBank, EMBL Protein Seqs – SWISS-PROT, PIR 3D structures – PDB Seq motifs – PROSITE Enzyme reactions – LIGAND Literature – LITDB Medline etc.,
DBGET
SRS SRS - Sequence Retrieval System - Data retrieval tool developed by EBI - Integrates 80 molecular biology DBs - An Open source software (Can be installed locally) SRS has an associated scripting language called Icarus
SRS SRS - Sequence Retrieval System - Data retrieval tool developed by EBI - Integrates 80 molecular biology DBs - An Open source software (Can be installed locally) SRS has an associated scripting language called Icarus
Genomics
Genomics What is Genomics? The study of genomes. In addition to the coding regions (genes), genomics comprise:  Control elements  Introns and exons  Gene clusters  Elements common to all chromosomes  Episomal elements
Genomics Benefits of Genomics: Genome sequencing helps in, - Identifying new genes (Gene discovery) - Looking at chromosome organization and structure - Finding gene regulatory seqs - Comparative genomics These in turn lead to advances in, - Medicine - Agriculture - Animal husbandry - Biotech - Evolution
Genomics Branches of Genomics, 1. Structural Genomics – Building genomic maps, 3D structures. 2. Functional Genomics – Transcriptomics, Proteomics, Metabolimomics, Enzymes 3. Comparative Genomics – Population distribution and Phenotypic associations 4. Evolutionary Genomics – Phylogenetic relationships 5. Pharmacogenomics – Interaction of drugs with genomes, Drug discovery
Genomics Tools required for Genomics, Robotics- Sequencing Statistics- Software High throughput assays- Microarrays High speed computing- Database work Bioinformatics- Algorithms, Graphics
Proteomics  Proteome is the protein complement of the genome  Proteomics is the study of proteomes  Human genome = 30,000 to 60,000 genes  Human proteome = 300,000 to 12,00,000  Reasons for Proteome>Genome: - Multiple ORFs - PTM - Internal peptide products
Proteomics Goal: Identify all the proteins expressed by a cell or tissue. Why to study proteomics?  Analysis of mRNA does not always correlate with expressed proteins  Some samples – Serum, Urine – can't be used for mRNA studies.  PTM can not be detected from mRNA  Location of proteins can not be known from mRNA
Proteomics Specialized proteomics 1. Expression Proteomics 2. Cell Map Proteomics 3. PTM 4. Protein- Protein interactions 5. Protein- Ligand Interactions 6. Protein structure
Proteomics Proteomics approach,  Separation of proteins using 2D electrophoresis.  Stain gel  Excise spots of interest  Digest with trypsin  Characterize peptides by MS/MALDI TOF  Compare peptide seqs with database of seqs.  Identify the class of proteins
Proteomics Methods to study Protein-Protein interactions 1. Yeast 2 Hybrid 2. AP-MS (Affinity purification-MS) Protein Microarrays can use immobilized - Proteins - Peptides - Carbohydrates - Antibodies - Small molecules to study other interactions.
Proteomics Applications: 1. Protein mining 2. Differential expression profiling 3. Network mapping 4. Study protein modifications