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

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.

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

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.

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

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. 



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

Some key bioinformatics websites NCBI (The National Center for Biotechnology Information) http://www.ncbi.nlm.nih.gov/ EBI (The European Bioinformatics Institute) http://www.ebi.ac.uk/ UCSC Genome bioinformatics http://genome.ucsc.edu/ SwissProt/ExPASy (Swiss Bioinformatics Resource) http://www.expasy.org/ PDB (The Protein Databank) http://www.rcsb.org/pdb/ 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

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…

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

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

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.

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.

Visual Guidance (entry point)

Categorized Resources

Categories (example 1)

Categories (example 2)

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

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)

Querying All Databases

Finding Resources