The ExPASy Molecular Biology Server

History of changes, improvements and new features

February 16, 1996

We have added a new tool, SIM which computes a user defined number of best non-intersecting alignments between two sequences. The results of the alignment can be viewed graphically using the LALNVIEW program developed by Laurent Duret and which is currently available for Macs and UNIX.

Additional links have been added in the tools page, notably to the Weizmann Institute ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator and to the Garnier, Osgoodthorpe and Robson (GOR) secondary structure prediction method at SBDS.

The SeqAnalRef database now includes a section listing author's email and eventually also WWW home pages. It is also possible to access the links from a page displaying either a reference list or a single reference.

Amos has recently started to create a list of Biomolecular servers for his own usage, but as some people have asked to access this list (which is under construction), we are making it available from the ExPASy top page. Many other small changes were carried out in the last two months.

We thank you for using ExPASy (we have now reached a cumulative total of 4 million connections).

December 14, 1995

After 29 months of existence the ExPASy molecular biology server received a new logo, designed and produced by Nicolas Guex.

October 23, 1995

The Melanie page has been reorganised. With the announcement of release 2.1 of the Melanie II 2-D PAGE analysis software package, a complete up-to-date description of the software as well as a comprehensive tutorial are now available.

October 13, 1995

Links have been added between SWISS-PROT Escherichia coli K12 chromosomal entries and the EcoCyc database, the encyclopedia of E. coli Gene and Metabolism.

You can now seach in PROSITE by citation.

October 9, 1995

Some new features of ExPASy:

• Search in SWISS-PROT by citation - When you call this option, you are prompted to enter the name of a journal and optionally a volume number and/or a year. The program is written in such a way that you can enter either the full name of a journal or its official abbreviation.
• RandSeq - a new tool to generate random protein sequences.
• SWISS-PROT document haeinflu.txt - Index of Haemophilus influenzae RD chromosomal entries and gene names with links to the TIGR and EMBL servers.
• SWISS-PROT document submit.txt - Description of how to submit sequence data to the SWISS-PROT data bank.
• SWISS-PROT document aatrnasy.txt - List of aminoacyl tRNA synthetases.
• Swiss-Jokes - A new page to give access to our collection of jokes from the fields of molecular biology and of computing.

Many other changes have been done, such as the redesign of the Geneva local pages; the addition, in the tool page, of links to ProfileScan and to the Bipartite NLS Locator.

It should also be noted that when you search in SWISS-PROT by either description or by full text and that your seach criteria returns more than two entries, you can save these entries to a file on our anonymous FTP server (in the outgoing directory).

September 19, 1995

AACompIdent: New options - AACompIdent is a tool which allows the identification of a protein from its amino acid composition. It searches SWISS-PROT for proteins, whose amino acid compositions are closest to the amino acid composition given. A new option and a new constellation have been added to this tool:

A. Tagging option

With this option, the first 40 amino acid of each protein are printed in the result, instead of the protein name. One may optionnally also enter a tag (a short seuqnece, typically 3 to 8 residues) which will be matched with the sequences of the resulting proteins. Proteins matching the tag will be marked.

B. Free constellation

This is a free constellation, that is one may select any amino acid constellation he/she likes. One just have to fill in the composition values for the selected amino acids. The values will then be normalised, so that the total make 100 (percent).

September 4, 1995

A new page has been created: WORLD-2DPAGE is an index to all known federated 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.

July 22, 1995

A new tool has been implemented on ExPASy, ProtParam allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, extinction coefficient, estimated half-life, instability index and aliphatic index

The Journal of Biological Chemistry (JBC) has a WWW server where abstracts and full text of articles are made available. We are happy to announce the implementation of what we believe to be the first direct link in a sequence database between a reference and the full text version of a cited article. Recent JBC references are directly linked to the corresponding entry point in the JBC server. If you want to see such a link, take a look at reference 3 in SWISS-PROT entry KDSA_ECOLI.

The SWISS-PROT document file jourlist.txt which provides information on all the journals cited in that database, now contains links to WWW or Gopher servers set up by a variety of publishers of academic journals.

Two new SWISS-PROT document have been added, one is a nomenclature and index of peptidase sequences, the other is the list of Yeast Chromosome VI entries in SWISS-PROT

June 19, 1995

A new tool has been implemented on ExPASy, ScanProsite allows to either scan a protein sequence the occurence of patterns stored in the PROSITE database or to scan the SWISS-PROT database - including weekly releases - for the occurence of a pattern.

We are happy to announce a new ""service"" Swiss-Quiz The principle of this quiz is to answer to 10 randomly chosen questions relative to the fields of molecular biology, biochemistry and genetics. Each month, we will randomly pick up one person among all those that have obtained a perfect score (and it's not so easy !) and will send that person some delicious Swiss chocolate !

Links have been added from SWISS-PROT to the Saccharomyces genomic database (SacchDb) at Stanford.

A new SWISS-PROT document has been added, it is a nomenclature and index of allergen sequences.

May 26, 1995

A new service is available: SWISS-2DSERVICE. The Two-Dimensional Gel Electrophoresis Laboratory of Geneva, Switzerland, is running a highly reproducible method for the two-dimensional separation of proteins. The laboratory now provides a 2-D PAGE service to which you may send your samples for analysis. This service includes analytical and preparative high-resolution 2-D PAGE, electrotransfer on membranes and/or amino acid composition.

May 17, 1995

New link in the Tools page to the multiple sequence alignment at Washington University.

May 11, 1995

Two links have been added to the SWISS-PROT entries. The first one directly submits a request to Swiss-Model for a 3D model of the current SWISS-PROT protein. The result is then sent back by e-mail. The second one allows to perform a sequence alignment with the current sequence, using NCBI's Basic Local Alignment Search Tool. This link is especially interesting in the virtual SWISS-PROT entries produced by the Translate tool.

May 5, 1995

We announce a new service, SWISS-FLASH, that reports news of databases, software and services developments from the Swiss biocomputing groups responsible for the ECD, ENZYME, LISTA, PROSITE, SeqAnalRef, SWISS-2DPAGE, SWISS-3DIMAGE and SWISS-PROT databases; the Melanie software package; the WWW ExPASy server; the SWISS-Model, SWISS- Shop and other network-based computational tools; and the SWISS-2DSERVICE services. If you subscribe to this service, you will automatically get the SWISS-Flash bulletins by electronic mail.

The SWISS-3DIMAGE database has been completely reorganised and indexed. The database is now searchable in the same way as the other SWISS-*** databases. We now also supply pictures in JPEG format, in addition to GIF and SGI. The images may still be downloaded by FTP.

Links to REBASE points now the version maintained at John Hopkins, whose layout is nicer than our own text based version !

April 19, 1995

We added Translate, a new tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.

Most of the pages in the server have been "refreshed" to make them more readable.

March 21, 1995

Links have been added from SWISS-PROT to the LISTA database of budding yeast (Saccharomyces cerevisiae) genes coding for proteins prepared under the supervisation of Patrick Linder.

March 7, 1995

Links have been added from SWISS-PROT to the HSSP database of structure-sequence alignments from the Protein Design Group, EMBL, Heidelberg.

March 2, 1995

During the last two months, various links have been added:

• from SWISS-PROT to the SubtiList and YEPD databases
• from ENZYME to PROSITE and to the Ligand database in Kyoto
• internally from PROSITE entries to other relevant PROSITE entries

Links from SWISS-PROT to FlyBase use the new WWW server for that database.

Many new SWISS-PROT documents have been added.

The page on the Melanie 2-D PAGE analysis software has been completely redesigned and includes now a on-line tutorial, as well as a request for information form.

December 7, 1994

In order to help users navigate through the ExPASy server, we have added graphical examples. More will be added in the future. See for example: Celegans examples or the who's who on ExPASy page. Thanks to Brigitte Boeckmann for the illustrations.

October 31, 1994

ENZYME: the ENZYME Data Bank has been added to the ExPASy server. This database may be accessed by EC number, name, compound, cofactor, comment, or by browsing through the list of classes, subclasses and sub-subclasses. Any entry in SWISS-PROT that contains an EC number in the DE line has also a direct link to ENZYME (by clicking on the EC number).

October 20, 1994

New services:

• Swiss-Shop - a sequence allerting system for Swiss-Prot that allows you to automatically obtain new sequence entries relevant to your field(s) of interest.
• Swiss-Model - an automated knowledge-based protein modelling server.

Compute pI/Mw: the tool to compute pI and Mw now accepts also a list of ID/AC's.

SWISS-PROT: in PDB cross-reference lines, there is now a link called RASMOL, sending the PDB entry as a chemical / pdb MIME type. On Unix systems, if you add, in the file .mailcap in your home directory, a line of the form

chemical/pdb; rasmol %s

then RASMOL will automatically be launched to display the protein 3D structure. This works also with any other program which accepts PDB coordinates. On systems other than Unix, this may also be specified. See your browser's manual.

October 13, 1994

The SWISS-PROT top page has been re-modeled. A number of new functionalities and documents have been added.

October 7, 1994

New tools have been added:

• Amino acid composition similarity search - the search may now also be performed from a given SWISS-PROT entry, whose amino acid composition will be compared with the whole SWISS-PROT database.
• Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT ID or AC, or for a given sequence.

October 5, 1994

The gels run during the 2-D PAGE courses in Geneva are now displayed on the server.

September 29, 1994

SWISS-2DPAGE: protein maps now have a pI/Mw scale.

SeqAnalRef: the Sequence Analysis Bibliographic Reference database has been added to the ExPASy server. This database may be accessed by keyword, by reference identifier, by author and by full text search.

List of on-line experts: in SWISS-PROT and PROSITE top pages, a list of on-line experts gives you the possibility to directly send questions to any of the listed experts. The list is ogranized by subjects.

SWISS-PROT: new lists added:

• List of abbreviations for journals cited
• List of species has been made active
• Yeast Chromosome III entries in SWISS-PROT
• Nomenclature of extracellular domain
• List of on-line experts

PROSITE: new 3D line with active links to PDB.

September 26, 1994

In the tool AACompIdent for identifying a protein by its amino acid composition, options have been added. They allow to specify how many proteins should be displayed, as well as the pI and Mw range in which the search should be performed.

Also, some old bugs have now been corrected.

September 12, 1994

The tool AACompIdent for identifying a protein by its amino acid composition, has been corrected and is now supposed to work. If you still encounter problems, please send us a mail.

June 17, 1994

SWISS-PROT: added cross-references (DR lines) to GenBank.

June 16, 1994

SWISS-PROT: added cross-references (DR lines) to MaizeDB Maize Genome Database of the National Agricultural Library.

June 6, 1994

Added the PROSITE page: PROSITE entries may now be searched by description of sites and pattern, by accession number, by author, and soon by full text search.

June 3, 1994

Added the GuessProt tool to the tools page: you may now get the SWISS-PROT proteins closest to a given pI and Mw.

May 27, 1994

In SWISS-PROT entries, added links to GCRDb - the G-Protein--Coupled Receptor DataBase.

Added the list of nomenclature related references for proteins to the SWISS-PROT top page.

May 26, 1994

Added a new reference 2-D PAGE map of Platelet to SWISS-2DPAGE.

May 20, 1994

The SWISS-2DPAGE team is now organizing a 2-D PAGE training in Geneva once every three months.

May 18, 1994

Added the Yeast Chromosome XI list of proteins to the SWISS-PROT documentation page.

May 11, 1994

Tools: new page giving access to on-line analysis tools, such as BLAST, BLITZ, PROSITE search and amino acid composition analysis, and more to come in the future.

March 23, 1994

Added the list of restriction enzymes and methylases in SWISS-PROT top page.

March 22, 1994

The ExPASy WWW server has been upgraded to a SPARCServer 10/51. It should perform much faster now. If some features are not working, please tell us about.

March 18, 1994

The links to OMIM are now direct links to the OMIM hypertext server from GDB. Thanks to Keith Robison for informing me about it.

March 4, 1994

SWISS-2DPAGE: Added experimental Amino Acid Composition Similarity Search: you enter a protein's amino acid composition and the server will e-mail you the list of SWISS-PROT entries with similar compositions, sorted by decreasing similarity measure.

March 2, 1994

Added direct link to NCBI's BLAST Basic Local Alignment Search Tool (ExPASy and SWISS-PROT top pages).

March 1, 1994

Starting with release 28, SWISS-PROT keyword search will be performed on the main release as well as on the weekly updates.

In the SWISS-PROT page, added links to four additional active lists:

• Index of Escherichia coli K12 chromosomal entries in SWISS-PROT and their corresponding EcoGene cross-reference
• Index of Saccharomyces cerevisiae entries in SWISS-PROT and their corresponding gene designations
• Index of Caenorhabditis elegans entries in SWISS-PROT and their corresponding gene designations and WormPep cross-references
• Index of Dictyostelium discoideum entries in SWISS-PROT and their corresponding gene designations and DictyDB cross-references

February 23, 1994

Added two new reference 2-D PAGE maps: Macrophage Like Cell Line (U937) and Erythroleukemia Cell (ELC).

In a SWISS-2DPAGE entry, it is now possible to compute the theoretical pI and Mw of the protein.

February 14, 1994

Added SWISS-2DPAGE Map Selection: you select a 2-D PAGE reference gel, click on a spot and get information on the corresponding protein. See the SWISS-2DPAGE top page.

February 11, 1994

Added a new reference 2-D PAGE map of Cerebrospinal Fluid to SWISS-2DPAGE.

January 28, 1994

Added the bionet newsgroups.

January 25, 1994

Added an entry to SWISS-3DIMAGE images of crystallized proteins.

In SWISS-PROT entries which contain cross-references to PDB, added a cross-reference to SWISS-3DIMAGE. Try for example AAT_ECOLI.

January 24, 1994

Added full text search of the SWISS-PROT protein sequence database.

January 17, 1994

Added links to MEDLINE entries in SWISS-PROT, through NCBI's Entrez Server.

Added, in the SWISS-2DPAGE page, a link to the QUEST Protein Database Center.

December 1, 1993

Added a User Survey. Please help us inprove the server in participating to this survey.

Added a new reference 2-D PAGE map of Lymphoma to SWISS-2DPAGE.

November 23, 1993

Added link to BioBit 24, the BIO-NAUT Newsletter from November, 22, 1993, describing the World Wide Web.

November 18, 1993

Added links to the Maize Genome Database at Columbia, Missouri and to EMBnet Switzerland.

November 17, 1993

Added the list of overall Top Ten users in the ExPASy server Activity Reports page.

November 16, 1993

Added Images of crystallized proteins from this server.

Added links to Harvard Biological Laboratories, the Gene-Server at University of Houston, the EMBnet: Biocomputing in Europe, the biology servers index at USGS, Jackson Laboratory WWW server and Keith Robison's Molecular Biology WWW sampler.

October 12, 1993

Added a list of specialised documents to the SWISS-PROT top page, such as 7-transmembrane G-linked receptors, CD nomenclature for surface proteins of Human leucocytes and Vertebrate homeobox proteins. Some of these list give then direct access to corresponding SWISS-PROT entries.

October 8, 1993

Added links to the Caenorhabditis elegans and Mycobacterium databases at INRA (France).

Added a link to the ExPASy server activity reports.

October 4, 1993

Moved to the NCSA server.

September 28, 1993

Added the PDB Brookhaven Protein Data Bank of 3D structures. In SWISS-PROT, cross-references to PDB have now active links to the gopher server at Protein Data Bank. You may access the PDB entry or get the 3D image. Try for example the SWISS-PROT entry P00782.

September 27, 1993

Added the FLYBASE database of genetic and molecular data for Drosophila. In SWISS-PROT and EMBL, cross-references to FLYBASE are now active links. Therefore, SWISS-PROT has now active links to SWISS-2DPAGE, EMBL, PROSITE, REBASE, OMIM and FLYBASE. EMBL has active links to SWISS-PROT and FLYBASE.

Warning: due to the fact that the FLYBASE syntax has not yet been perfectly formalised, certain links may be empty and certain others links may be missing.

September 23, 1993

Added a link to the National Institute of Health Genobase Server to our top page.

September 21, 1993

Announced the ExPASy server and SWISS-2DPAGE release 0 to bionet.announce.

August 1, 1993

Installed the ExPASy molecular biology server, release 0, beta version.

Last modified 14/Dec/1995 by ROA