Data retrieval

1. Data Retrieval

2. Access to Distributed data
Biological data is widely distributed over the WWW.
Data can be retrieved by,
1. Search engines
2. Data retrieval tools

3. 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.

4. Leapfish

5. bing

6. 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.

7. Entrez
- WWW-based data retrieval system.
- Developed by NCBI (National Centre for Biotechnology
Information).
- Integrates information held in different DBs.

8. 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

9. Entrez

10. Entrez

11. 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.,

12. DBGET

13. 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

14. 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

15. Genomics

16. 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

17. 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

18. 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

19. Genomics
Tools required for Genomics,
Robotics- Sequencing
Statistics- Software
High throughput assays- Microarrays
High speed computing- Database work
Bioinformatics- Algorithms, Graphics

20. 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

21. 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

22. Proteomics
Specialized proteomics
1. Expression Proteomics
2. Cell Map Proteomics
3. PTM
4. Protein- Protein interactions
5. Protein- Ligand Interactions
6. Protein structure

23. 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

24. 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.

25. Proteomics
Applications:
1. Protein mining
2. Differential expression profiling
3. Network mapping
4. Study protein modifications