In particular, the ExPASy BLAST interface now allows to launch a sequence similarity search against the UniRef clusters UniRef100, UniRef90 and UniRef50.
Implicit links to UniRef50 and UniRef90 have been added to the NiceProt view of UniProt knowledgebase entries.
In the NiceProt view for Swiss-Prot/TrEMBL entries we have added implicit links to the Swiss-Model repository of 3D homology models (SMR).
It is now possible to submit all splice isoforms annotated in one Swiss-Prot entry to a multiple alignment, or to retrieve the sequences of all these isoforms.
The legends for the Biochemical Pathways have been made available in html and pdf format.
Whenever reference is made to the Transport Commission (TC) System in Swiss-Prot comments lines (CC), a link is added from the NiceProt view to the Transport Protein Database (example: P37905).
=== ExPASy ===
=== TOOLS ===
Two tools have been added to our collection of sequence analysis and proteomics tools:
=== SWISS-PROT ===
Similarly, in the "Cross-references" section, the names of the databases to which an entry is cross-referenced are linked to the corresponding sections in the document dbxref.txt (List of databases cross-referenced in SWISS-PROT).
=== SWISS-2DPAGE ===
New cross-references, reference maps, and a document have been added:
The keyword "Complete proteome" has been introduced to all SWISS-PROT/TrEMBL entries describing a protein which is thought to be expressed by an organism whose genome has been completely sequenced. This keyword is so far only used for microbial (bacterial and archaeal) proteins. A complete set of proteins from a microbial genome can therefore be obtained using this keyword across SWISS-PROT and TrEMBL.
A new and improved version of the NiceProt view of SWISS-PROT is available (example). Some of its new features are:
SWISS-PROT release statistics are now available for every update of the database. Among other parameters, statistics about database growth, average sequence lengths and amino acid composition, taxonomic origin, journal citations and database cross-references are presented, including some graphics.
A new view is available within the SRS Sequence Retrieval System. It displays, for each protein corresponding to a user query, gene name(s) and organism (in addition to the parameters ID, AC, description and sequence length which are displayed by the default view "Short description"). This new view is entitled "Long description" and is available from the menu "Use view ..." in the SRS query form.
The SIB Blast interface (accessible also via "Quick BLAST" or from the bottom of every SWISS-PROT/ TrEMBL entry) now offers the possibility to restrict the similarity search by using taxonomic criteria. A "Taxonomic View" of the results can also be obtained via the BLAST result page.
L'équipe Swiss-Prot a le plaisir de vous présenter le premier article de "Protéines à la Une", sa nouvelle rubrique de vulgarisation scientifique dédiée aux protéines qui font parler d'elles dans l'actualité.
The additional isoform entries have been added to the SWISS- PROT/TrEMBL databases underlying the BLAST server at SIB/CSCS Switzerland, and ScanProsite. Gradually, all other tools on ExPASy will be modified to handle splice isoforms. The NiceProt view of SWISS-PROT/TrEMBL provides links from the isoform name in the feature table (example: Q01432) to a page displaying the sequence of the corresponding isoform.
A Genomic Proximity Viewer is available for those microbial genomes where an ORF numbering system exists. For those organisms, it is possible to click on the ORF name in the SWISS-PROT/TrEMBL GN (gene) lines to obtain a list of proteins encoded by genes in proximity (example: P46448). The tool is also accessible from the HAMAP complete proteome pages of those organisms. Example: Borrelia burgdorferi.
SWISS-PROT:
ExPASy:
The following tools are available:
Database Tool Example --------------------------------------------------------------------------- SWISS-PROT NiceProt https://www.expasy.ch/cgi-bin/niceprot.pl?P14060 SWISS-2DPAGE Nice2DPage https://www.expasy.ch/cgi-bin/nice2dpage.pl?P00938 PROSITE NiceSite https://www.expasy.ch/cgi-bin/nicesite.pl?PS00661 https://www.expasy.ch/cgi-bin/nicedoc.pl?PDOC00566 ENZYME NiceZyme https://www.expasy.ch/cgi-bin/nicezyme.pl?2.4.1.1We have now changed all our tools and database search programs on ExPASy to display the 'Nice' version of a database entry by default. The programs displaying database entries in their original text formats continue to be maintained, and links are available from the 'Nice' views to the corresponding get-xxx-entry programs (e.g. get-sprot-entry).
If you maintain pages with links to entries from the above-mentioned databases, you might be interested to update these links to use the 'Nice' View if you prefer this representation to the original format. Otherwise you are, of course, completely free to keep the get-xxx-entry links.
Please make sure to update all pointers using the old domain expasy.hcuge.ch,
which was replaced by
http://www.expasy.ch/ in March 1997 (!). The 'expasy.hcuge.ch'
address might be disabled in the near future.
Users can now also use (in addition to the home page and ExPASy Index) the newly created clickable ExPASy site map to find useful tools, documents and services available on our server, and to find out about functional links between them.
A new documentation page has been created which presents a complete table of documents available on ExPASy.
TagIdent can now search in SWISS-PROT, TrEMBL or both databases. It is also possible to perform an additional scan of a short sequence tag against all fragments contained in the database(s), even if pI and Mw cannot be computed for these proteins.
MultiIdent (identification using pI, MW, amino acid composition, sequence tag and peptide mass fingerprinting data) is available for constellation 2 (Ala, Ile, Pro, Val, Arg, Leu, Ser, Asx, Lys, Thr, Glx, Gly, Met, His, Phe and Tyr. (Asp+Asn=Asx; Gln+Glu=Glx; Cys and Trp are not considered)) and constellation 4 (like constellation 2, but Gly is not considered).
You can combine all the fields with logical operators and achieve queries like:
Five databases are indexed: SWISS-PROT, TrEMBL, TrEMBL_NEW, PROSITE, and ENZYME. SWISS-PROT and TrEMBL are updated on a weekly basis so that the set of these two databases stays non-redundant.
TrEMBL entries are now fully accessible on ExPASy via a cgi-script. The hypertext version of TrEMBL contains links to various databases and allows direct access to sequence analysis tools such as Swiss-Model, Blast, ProtParam, ProtScale, Compute pI/Mw and PeptideMass, as is the case for SWISS-PROT.
If you wish to link to a TrEMBL entry, you can use the following URL:
http://www.expasy.ch/cgi-bin/get-sprot-entry?<TrEMBL-AC>
e.g. to create a link to TrEMBL entry Q00061, use:
The tool which allows you to visualize and highlight the subsequence corresponding to a line in a SWISS-PROT feature table (FT) has been improved and is now using colour to highlight the subsequences in question. Example: in FA9_HUMAN:
FT DOMAIN 93 129 EGF-LIKE 1, CALCIUM-BINDING (POTENTIAL).
In the tools page, you can now choose between 5 different interfaces to BLAST servers in Switzerland, the USA and Germany:
For direct BLAST submission from a SWISS-PROT entry (icons at the bottom of the page displaying an entry - example), you have the choice between the servers at NCBI and EMBNet-CH.
The following documents have been added to the list of SWISS-PROT documents:
In the new version of Swiss-Shop, some new features have been added:
As before, you can either launch a sequence/pattern based search or a keyword based search.
Furthermore, we now offer you 4 different output formats. You can choose to receive the sequences matching your query
The following tools have been improved, offering numerous additional features:
For PeptideMass, Compute pI/Mw, AACompSim and all the above-mentioned tools, documentation and references have been added and the submission forms have been reformatted and improved.
The old URL remains valid for some time.
CC -!- DATABASE: NAME=CD40Lbase; NOTE=European CD40L defect database; CC WWW="HTTP://www.expasy.ch/cd40lbase/"; CC FTP="ftp.expasy.ch/databases/cd40lbase".
A new tool is available from the Tools page: The PeptideMass Peptide Characterisation Software. This program is designed to calculate the theoretical masses of peptides generated by the chemical or enzymatic cleavage of proteins, to assist in the interpretation of peptide mass fingerprinting and peptide mapping experiments. Protein sequences can be provided by the user or can be a code name for a protein in the SWISS-PROT protein database. When proteins of interest are specified from SWISS-PROT, the program considers all annotations for that protein in the database, and uses these in order to generate the correct peptide masses and warn users about peptides that are not likely to be found when undertaking peptide mass fingerprinting. Many protein post-translational modifications which affect the masses of peptides can thus be taken into consideration.
In PROSITE and Enzyme, we have added the possibility to save all referenced SWISS-PROT entries to a file on our anonymous FTP server (in the outgoing directory).
The Compute pI/Mw tool has been included in the list of sequence analysis tools that can be directly accessed from a SWISS-PROT entry.
Two new SWISS-PROT documents are available:
- humchr20.txt
- an index of protein sequence entries encoded on human chromosome 20
- tisslist.txt
- a list of the currently valid values for the "TISSUE" topic of the
RC line type in SWISS-PROT.
In ec2dtosp.txt, an index of E. coli Gene-protein database (ECO2DBASE) entries referenced in SWISS-PROT, we have established direct links to ECO2DBASE, and SWISS-PROT entries now also contain links to ECO2DBASE.
At the end of each page displaying a SWISS-PROT entry we have added links to our sequence analysis tools ProtParam and ProtScale,which allows the user to directly submit the SWISS-PROT sequence to these tools.
FT DOMAIN 93 129 EGF-LIKE 1, CALCIUM-BINDING (POTENTIAL).
Links have been added between relevant SWISS-PROT entries and the 2D gel protein databases at Harefield.
A new SWISS-PROT document has been added which describes the nomenclature of glycosyl hydrolases (GH) and that includes an index of sequences that belong to the various GH families.
A PC (MS-Windows) version of LALNVIEW (graphical viewer for pairwise alignments) is now available.
Nicolas Guex has produced a new logo for PROSITE.
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).
You can now seach in PROSITE by citation.
Many other changes have been done, such as the redesign of the Geneva local pages; the addition, in the tool page, of a link to ProfileScan.
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).
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
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.
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 !
Most of the pages in the server have been "refreshed" to make them more readable.
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.
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 %sthen 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.
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:
PROSITE: new 3D line with active links to PDB.
Also, some old bugs have now been corrected.
Added the list of nomenclature related references for proteins to the SWISS-PROT top page.
In the SWISS-PROT page, added links to four additional active lists:
In a SWISS-2DPAGE entry, it is now possible to compute the theoretical pI and Mw of the protein.
In SWISS-PROT entries which contain cross-references to PDB, added a cross-reference to SWISS-3DIMAGE. Try for example AAT_ECOLI.
Added, in the SWISS-2DPAGE page, a link to the QUEST Protein Database Center.
Added a new reference 2-D PAGE map of Lymphoma to SWISS-2DPAGE.
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.
Added a link to the ExPASy server activity reports.