Presentation on theme: "ExPASy - Expert Protein Analysis System The bioinformatics resource portal and other resources An Overview."— Presentation transcript:
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 benchbut the huge increase in the scale of data being produced in this genomic era has seen a need to utilize computational processing.
3 BioinformaticsFollowing 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 sequenceProtein sequence determines protein structureProtein structure determines protein function
4 BioinformaticsWidely 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 BioinformaticsThe 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 goalHowever, 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 BioinformaticsThe 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.
8 Some key bioinformatics websites NCBI (The National Center for Biotechnology Information)EBI (The European Bioinformatics Institute)UCSC Genome bioinformaticsSwissProt/ExPASy (Swiss Bioinformatics Resource)PDB (The Protein Databank)You are using someone else’s computerYou are (probably) getting a reduced set of options or capacityServers 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 databasesMedline/OMIMGenbank/Genpept/StructuresBLAST server(s)Many flavors of blastDraft Human GenomeMuch more…
10 EBI (The European Bioinformatics Institute) SRS (sequence retrieval system) database interfaceEMBL, SwissProt, and many moreMany server-based toolsClustalW, 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 sourcesSwissProt 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 OverviewHistorically 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:GenomicsPhylogeny/evolutionSystems biologyPopulation geneticsTranscriptomicsetc.
13 ExPASy Overview (cont.) The individual resourcesdatabasesweb-based and downloadable software toolsare 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.