ExPASy server

The importance of this information on biochemical reactions is emphasized by the fact that an image of the poster is also accessible on the ExPASy seiwer [20]. However, for this purpose, the poster has only been scanned. The ExPASy server provides a static image of the information on this web site, augmented only by links to additional information. 

ExPASy Server Roche Applied Science Biochemical Pathways... 

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

The expasy server [33] offers references to many Web sites for protein sequence analysis and secondary structure prediction. 

In this Section, we describe a number of protein identification and characterisation tools available on the World-Wide Web (WWW). All the tools described here are accessible from the ExPASy tools page http //www. expasy.org/tools/, which is constantly updated. Particular emphasis will be given to the programs provided on the ExPASy proteomics server [23, http //www.expasy.org]. Note that currently the Geneva ExPASy server (www. 

Increasing reproducibility of available separation techniques and sensitivity and affordability of mass spectrometers, as well as the desire and need to automate the identification process, have caused peptide mass fingerprinting and MS/MS sequencing to gain importance and to become the method of choice for many proteomics laboratories. Several tools are available to assist users in the interpretation of mass spectrometry data. Peptldent (http //www.expasy.org/tools/peptident.html) on the ExPASy server follows the concept of the other tools from the ExPASy proteomics suite, in that it takes into account annotation available in the SWISS-PROT/TrEMBL database, in particular as post-translational modifications and processing are concerned. The user can paste peptide masses (monoisotopic or average) into the Peptldent form, but peptide mass data can also be uploaded from a file on the user s local computer. Supported file formats are .pkm ... 

SWISS-PROT [25, http //www.expasy.org/sprot/] is a curated protein sequence database which provides a high level of annotation, such as the description of a protein s function, its domain structure, PTMs, conflicts between literature references and variants. It also provides a minimal level of redundancy, a high level of integration with other biomolecular databases, and an extensive external documentation. Created in 1986, it now includes more than 100 000 entries from more than 7000 different species. SWISS-PROT is available from more than 100 WWW servers world-wide and its main host is the ExPASy server. 

There are many such databases available. Their contents vary a lot in terms of the range of interest, number of entries and type of information. As it is impossible to be exhaustive here, we recommend readers to consult the updated list on the World-Wide Web, maintained by Amos Bairoch on the ExPASy server (http //www.expasy.org/alinks.html). 

ExPASy Server (2D liver, plasma, etc. SWISS-(PROT, 2DPAGE, 3D1MAGE), BIOSCI, Melanie software)... 

ExPASy (Expert lYotein Analysis System) molecular biology server http //WWW. expasy. ch... 

Gasteiger, E. Gattiker, A. Hoogland, C. Ivanyi, I. Appel, R. D. Bairoch, A. ExPASy The proteomics server for in-depth protein knowledge and analysis. Nucl. Acids Res. 2003,31, 3784-3788. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

Protein primary structure databases include the following ExPASy Molecular Biology Server (Swiss-Prot) expasy.ch/ Protein Information resources (PIR) pir.georgetown.edu Protein Research Foundation (PRF) prf.or.jp/en/os.html. 

High-speed identification from either PMF or MS/MS data can be achieved from non-redundant protein databases (Mann ef a/., 2001). These often include valuable annotations giving insight into functions of isolated and identified proteins. Many of these databases, such as NCBInr (National Centre for Biotechnology Information) and Swiss Prot (ExPASy Molecular Biology Server), can be used for protein identification. 

Protein Explorer is a knowledge base with introductory information on many topics about protein structure, such as the origins and limitations of 3D protein structure data, specific oligomers vs. crystal contacts, hydrogen bonds, cahon-pl interactions, etc. Protein Explorer is more user-friendly than the comparable software RASMOL, also available on servers such as ExPASy. 

NCBI education page on bioinformatics http //www.ncbi.nlm.nih.gov/education/index.html ExPASy Molecular Biology Server http //www.expasv.ch/... 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

A number of useful computational tools have been developed for predicting the identity of unknown proteins based on the physical and chemical properties of amino acids and vice versa. Many of these tools are available through the Expert Protein Analysis System (ExPASy) at http //www.expasy.ch (Appel et al., 1994) and other servers. 

The comprehensive molecular biology server, ExPASy (Expert Protein Analysis System), provides Proteomic tools (http //www.expasy.ch/tools) that can be accessed directly or from the ExPASy home page by selecting Identification and Characterization under Tools and Software Packages. The Protein identification and characterization tools of the Proteomics tools (Figure 11.4) provide facilities to ... 

A number of servers offer various methods to predict secondary structures of proteins. Secondary structure prediction of ExPASy Proteomic tools (http //... 

A number of Web sites offer services in the secondary structure predictions of proteins using different approaches with varied accuracy. The Secondary structure prediction of ExPASy Proteomic tools (http //www.expasy.ch/tools/) provides pointers to different Web servers for predicting secondary structures of proteins. The ProtScale of ExPASy Proteomic tools produces conformational profiles by plotting statistical scales of various parameters (e.g., Chou and Fasman s conformational propensities, Levitt s conformational parameters) against residue positions. 

Figure 12.16. ProSite search by different servers. The ProSite searches for Pig ribonuc-lease are performed by ScanProsite of ExPASy, PPSearch of EBI, and ProfileScan. Identical results with slightly different outputs are obtained.

The ProtSite search can be conducted at ScanProsite tool (selecting Scan a sequence for the occurrence of PROSITE patterns) of ExPASy Proteomic tools (http //www.expasy.ch/tools/scnpsite.html), or PPSearch of EBI (http //www2.ebi.ac. uk/ppsearch/) or ProfileScan server (http //www.isrec.isb-sib.ch/software/PFSCAN form.html). On the search form, paste the query sequence, select options (e.g., display in PPSearch and databases in ProfileScan) and click the Run/Start the Scan button. The search results are returned (after clicking SEView applet button in ProfileScan) with different outputs as shown in Figure 12.16. 

Eukaryotic polymerase II promoter server Exlnt database ExPASy, tools FlyBase GDB GenBank,... 

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