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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.

+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

+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/

+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

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

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