1. ExPASy - Expert Protein Analysis System The bioinformatics resource portal and other resources
An Overview

2. Bioinformatics Bioinformatics in the context of molecular biology
Traditionally, molecular biology research was carried out entirely at the experimental laboratory bench
but the huge increase in the scale of data being produced in this genomic era has seen a need to utilize computational processing.

3. Bioinformatics
Following on from the explosion in the volume of genomic data, similar increase in data have been observed in the fields of proteomics, transcriptomics and metabalomics.
There are three central biological processes around which bioinformatics tools have been developed:
DNA sequence determines protein sequence
Protein sequence determines protein structure
Protein structure determines protein function

4. Bioinformatics
Widely defined, bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyze and merge biological data.

5. Bioinformatics
The ultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of data and obtain a clearer insight into the fundamental biology of organisms.
The integration of information learned about these key biological processes should allow us to achieve the ultimate goal
However, the molecular biology of an organism is a very complex issue even with research being carried out at different levels including the genome, proteome, transcriptome and metabalome levels, more can also be looked at in an integrative comu

6. Bioinformatics
The challenge facing the bioinformatics community today is:
Intelligent and efficient storage of this mass of data.
Development of tools to allow the extraction of meaningful biological information. 



7. Examples of Bioinformatics
Database interfaces
Genbank/EMBL/DDBJ, Medline, SwissProt, PDB, …
Sequence alignment / Multiple sequence alignment
BLAST, FASTA, Clustal, Muscle
Gene finding
Genscan, GenomeScan, GeneMark, GRAIL
Protein Domain analysis and identification
pfam, BLOCKS, ProDom,
Pattern Identification/Characterization
Gibbs Sampler, AlignACE, MEME
Protein Folding prediction
PredictProtein, SwissModeler

8. Some key bioinformatics websites
NCBI (The National Center for Biotechnology Information)
EBI (The European Bioinformatics Institute)
UCSC Genome bioinformatics
SwissProt/ExPASy (Swiss Bioinformatics Resource)
PDB (The Protein Databank)
You are using someone else’s computer
You are (probably) getting a reduced set of options or capacity
Servers are great for sporadic or proof-of-principle work, but for intensive work, the software should be obtained and run locally

9. NCBI (The National Center for Biotechnology Information)
Entrez interface to databases
Medline/OMIM
Genbank/Genpept/Structures
BLAST server(s)
Many flavors of blast
Draft Human Genome
Much more…

10. EBI (The European Bioinformatics Institute)
SRS (sequence retrieval system) database interface
EMBL, SwissProt, and many more
Many server-based tools
ClustalW, DALI, …

11. SwissProt/ExPASy Curation!
Error rate in the information is greatly reduced in comparison to most other databases.
Extensive cross-linking to other data sources
SwissProt is the ‘gold-standard’ by which other databases can be measured, and is the best place to start if you have a specific protein to investigate

12. ExPASy Overview
Historically Expasy has been one of the main online bioinformatics resources for proteomics.
Evolving into an extensible and integrative portal for accessing many scientific resources, databases, and software in different areas of life sciences:
Genomics
Phylogeny/evolution
Systems biology
Population genetics
Transcriptomics
etc.

13. ExPASy Overview (cont.)
The individual resources
databases
web-based and downloadable software tools
are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.
Single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions.

14. Visual Guidance (entry point)

15. Categorized Resources

16. Categories (example 1)

17. Categories (example 2)

18. Categories Proteomics Genomics Protein sequences and identification
Structural bioinformatics
System biology
Phylogeny/evolution
Population genetics
Transcriptomics
Biophysics
Imaging
IT infrastructure
Drug design
Proteomics
Protein sequences and identification
Mass spectrometry and 2-DE data
Protein characterization and function
Families, patterns and profiles
Post-translational modification
Protein structure
Protein-protein interaction
Similarity search/alignment
11 Categories
Genomics
Sequence alignment
Similarity search
Characterization/annotation

19. Advanced search/query
Query all databases (i.e. launch a query across several SIB resources)
Find resources: discover resources hosted on the portal (incl. auto-completion)

20. Querying All Databases

21. Finding Resources