Expasy

Expert Protein-Analysis System

Logo Expasy 2020

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. 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.

## Search engine

[edit]

Queries of Expasy allow:

1. parallel searches SIB databases through a single search
2. aggregated search results from the complete set of >160 resources accessible from the portal.[1]

Expasy provides up-to-date information from the most recent release of each resources.

The terms used in Expasy are based on the EDAM comprehensive ontology.[2]

## History

[edit]

Expasy was created in August 1993. Originally, it was called ExPASy (Expert Protein Analysis System) and acted as a proteomics server to analyze protein sequences and structures and two-dimensional gel electrophoresis (2-D Page electrophoresis).[3] Among others, ExPASy hosted the protein sequence knowledge base, UniProtKB/Swiss-Prot, and its computer annotated supplement, UniProtKB/TrEMBL.[4]

ExPASy was the first website of the life sciences and among the first 150 websites in the world. As of 5 April 2007[update], ExPASy had been consulted 1 billion times since its installation on 1 August 1993.[5]

In June 2011, it became the SIB ExPASy Bioinformatics Resources Portal: a diverse catalogue of bioinformatics resources developed by SIB Groups.[6] The current version of Expasy was released in October 2020.[7][8]

## Notes and references

[edit]

1. ^ "SIB Resources". sib.swiss. Retrieved 27 October 2020.
2. ^ Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, et al. (May 2013). "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats". Bioinformatics. 29 (10): 1325–32\. doi:10.1093/bioinformatics/btt113. PMC 3654706. PMID 23479348.
3. ^ Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (July 2003). "ExPASy: The proteomics server for in-depth protein knowledge and analysis". Nucleic Acids Research. 31 (13): 3784–8\. doi:10.1093/nar/gkg563. PMC 168970. PMID 12824418.
4. ^ "UniProtKB/Swiss-Prot - SIB Swiss Institute of Bioinformatics | Expasy". www.expasy.org. Retrieved 15 March 2024.
5. ^ ExPASy: SIB Bioinformatics Resource Portal
6. ^ Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, et al. (July 2012). "ExPASy: SIB bioinformatics resource portal". Nucleic Acids Research. 40 (Web Server issue): W597-603. doi:10.1093/nar/gks400. PMC 3394269. PMID 22661580.
7. ^ Duvaud, Séverine; Gabella, Chiara; Lisacek, Frédérique; Stockinger, Heinz; Ioannidis, Vassilios; Durinx, Christine (13 April 2021). "Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users". Nucleic Acids Research. 49 (W1): W216 – W227. doi:10.1093/nar/gkab225. ISSN 0305-1048. PMC 8265094. PMID 33849055.
8. ^ "Discover the new Expasy.org, the Swiss Bioinformatics Resource Portal". sib.swiss. Retrieved 26 October 2020.

## External links

[edit]

* Official website

* v
* t
* e

Bioinformatics

Databases|

* Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
* Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
* Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
* Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network

Software|

* BLAST
* Bowtie
* Clustal
* EMBOSS
* HMMER
* MUSCLE
* PANGOLIN
* SAMtools
* SOAP suite
* TopHat

Other|

* Server: ExPASy
* Rosalind (education platform)

Institutions|

* Broad Institute
* Computational Biology Department (CBD)
* Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
* Database Center for Life Science (DBCLS)
* DNA Data Bank of Japan (DDBJ)
* European Bioinformatics Institute (EMBL-EBI)
* European Molecular Biology Laboratory (EMBL)
* Flatiron Institute
* J. Craig Venter Institute (JCVI)
* Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
* US National Center for Biotechnology Information (NCBI)
* Japanese Institute of Genetics
* Netherlands Bioinformatics Centre (NBIC)
* Philippine Genome Center (PGC)
* Scripps Research
* Swiss Institute of Bioinformatics (SIB)
* Wellcome Sanger Institute
* Whitehead Institute

Organizations|

* African Society for Bioinformatics and Computational Biology (ASBCB)
* Australia Bioinformatics Resource (EMBL-AR)
* European Molecular Biology network (EMBnet)
* International Nucleotide Sequence Database Collaboration (INSDC)
* International Society for Biocuration (ISB)
* International Society for Computational Biology (ISCB)
* Student Council (ISCB-SC)
* Institute of Genomics and Integrative Biology (CSIR-IGIB)
* Japanese Society for Bioinformatics (JSBi)

Meetings|

* Basel Computational Biology Conference‎ ([BC2])
* European Conference on Computational Biology (ECCB)
* Intelligent Systems for Molecular Biology (ISMB)
* International Conference on Bioinformatics (InCoB)
* International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
* ISCB Africa ASBCB Conference on Bioinformatics
* Pacific Symposium on Biocomputing (PSB)
* Research in Computational Molecular Biology (RECOMB)

File formats|

* CRAM format
* FASTA format
* FASTQ format
* NeXML format
* Nexus format
* Pileup format
* SAM format
* Stockholm format
* VCF format
* GFF format
* GTF format

Related topics|

* Computational biology
* List of biobanks
* List of biological databases
* Molecular phylogenetics
* Sequencing
* Sequence database
* Sequence alignment

* Category
* Commons

*[v]: View this template
*[t]: Discuss this template
*[e]: Edit this template