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Amos Marc Bairoch - One of the best experts on this subject based on the ideXlab platform.

  • the universal protein resource uniprot
    Nucleic Acids Research, 2004
    Co-Authors: Amos Marc Bairoch, Rolf Apweiler, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the SWISS-PROT, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/SWISS-PROT, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

  • the swiss prot protein knowledgebase and expasy providing the plant community with high quality proteomic data and tools
    Plant Physiology and Biochemistry, 2004
    Co-Authors: Michel Schneider, Michael Tognolli, Amos Marc Bairoch
    Abstract:

    The SWISS-PROT protein knowledgebase provides manually annotated entries for all species, but concentrates on the annotation of entries from model organisms to ensure the presence of high quality annotation of representative members of all protein families. A specific Plant Protein Annotation Program (PPAP) was started to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Its main goal is the annotation of proteins from the model plant organism Arabidopsis thaliana. In addition to bibliographic references, experimental results, computed features and sometimes even contradictory conclusions, direct links to specialized databases connect amino acid sequences with the current knowledge in plant sciences. As protein families and groups of plant-specific proteins are regularly reviewed to keep up with current scientific findings, we hope that the wealth of information of Arabidopsis origin accumulated in our knowledgebase, and the numerous software tools provided on the Expert Protein Analysis System (ExPASy) web site might help to identify and reveal the function of proteins originating from other plants. Recently, a single, centralized, authoritative resource for protein sequences and functional information, UniProt, was created by joining the information contained in SWISS-PROT, Translation of the EMBL nucleotide sequence (TrEMBL), and the Protein Information Resource-Protein Sequence Database (PIR-PSD). A rising problem is that an increasing number of nucleotide sequences are not being submitted to the public databases, and thus the proteins inferred from such sequences will have difficulties finding their way to the SWISS-PROT or TrEMBL databases.

  • the swiss prot variant page and the modsnp database a resource for sequence and structure information on human protein variants
    Human Mutation, 2004
    Co-Authors: Yum Lina Yip, Alexandre Gattiker, Elisabeth Gasteiger, Holger Scheib, Alexander V Diemand, L Famiglietti, Amos Marc Bairoch
    Abstract:

    Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The SWISS-PROT protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the SWISS-PROT Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the SWISS-PROT knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly SWISS-PROT release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The SWISS-PROT variant pages are accessible from the NiceProt view of a SWISS-PROT entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP.

  • uniprot the universal protein knowledgebase
    Nucleic Acids Research, 2004
    Co-Authors: Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the SWISS-PROT, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar SWISS-PROT (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

  • expasy the proteomics server for in depth protein knowledge and analysis
    Nucleic Acids Research, 2003
    Co-Authors: Elisabeth Gasteiger, Alexandre Gattiker, Ron D. Appel, Christine Hoogland, Ivan Ivanyi, Amos Marc Bairoch
    Abstract:

    The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.

Rolf Apweiler - One of the best experts on this subject based on the ideXlab platform.

  • the universal protein resource uniprot
    Nucleic Acids Research, 2004
    Co-Authors: Amos Marc Bairoch, Rolf Apweiler, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the SWISS-PROT, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/SWISS-PROT, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

  • uniprot the universal protein knowledgebase
    Nucleic Acids Research, 2004
    Co-Authors: Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the SWISS-PROT, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar SWISS-PROT (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

  • the swiss prot protein knowledgebase and its supplement trembl in 2003
    Nucleic Acids Research, 2003
    Co-Authors: Brigitte Boeckmann, Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Marieclaude Blatter, Anne Estreicher, Maria Jesus Martin, Karine Michoud, Claire Odonovan, Isabelle Phan
    Abstract:

    The SWISS-PROT protein knowledgebase (http:// www.expasy.org/sprot/ and http://www.ebi.ac.uk/ swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at SWISS-PROT@expasy.org.

  • functional information in swiss prot the basis for large scale characterisation of protein sequences
    Briefings in Bioinformatics, 2001
    Co-Authors: Rolf Apweiler
    Abstract:

    With the rapid growth of sequence databases, there is an increasing need for reliable functional characterisation and annotation of newly predicted proteins. To cope with such large data volumes, faster and more effective means of protein sequence characterisation and annotation are required. One promising approach is automatic large-scale functional characterisation and annotation, which is generated with limited human interaction. However, such an approach is heavily dependent on reliable data sources. The SWISS-PROT protein sequence database plays an essential role here owing to its high level of functional information.

  • proteome analysis database online application of interpro and clustr for the functional classification of proteins in whole genomes
    Nucleic Acids Research, 2001
    Co-Authors: Rolf Apweiler, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola Mulder, Margaret Biswas, Isabelle Phan
    Abstract:

    The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes (http://www.ebi.ac.uk/proteome/). The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31–67% (InterPro statistics) of the proteins from each of the complete genomes. CluSTr covers the three complete eukaryotic genomes and the incomplete human genome data. The Proteome Analysis Database is accompanied by a program that has been designed to carry out InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

Brigitte Boeckmann - One of the best experts on this subject based on the ideXlab platform.

  • the universal protein resource uniprot
    Nucleic Acids Research, 2004
    Co-Authors: Amos Marc Bairoch, Rolf Apweiler, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the SWISS-PROT, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/SWISS-PROT, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

  • uniprot the universal protein knowledgebase
    Nucleic Acids Research, 2004
    Co-Authors: Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the SWISS-PROT, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar SWISS-PROT (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

  • the swiss prot protein knowledgebase and its supplement trembl in 2003
    Nucleic Acids Research, 2003
    Co-Authors: Brigitte Boeckmann, Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Marieclaude Blatter, Anne Estreicher, Maria Jesus Martin, Karine Michoud, Claire Odonovan, Isabelle Phan
    Abstract:

    The SWISS-PROT protein knowledgebase (http:// www.expasy.org/sprot/ and http://www.ebi.ac.uk/ swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at SWISS-PROT@expasy.org.

  • the swiss prot protein sequence data bank current status
    Nucleic Acids Research, 1994
    Co-Authors: Amos Marc Bairoch, Brigitte Boeckmann
    Abstract:

    SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1988, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. The SWISS-PROT protein sequence data bank consist of sequence entries. Sequence entries are composed of different lines types, each with their own format. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL Nucleotide Sequence Database. A sample SWISS-PROT entry is shown in Figure 1.

  • the swiss prot protein sequence data bank
    Nucleic Acids Research, 1991
    Co-Authors: Amos Marc Bairoch, Brigitte Boeckmann
    Abstract:

    SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1988, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library

Elisabeth Gasteiger - One of the best experts on this subject based on the ideXlab platform.

  • the universal protein resource uniprot
    Nucleic Acids Research, 2004
    Co-Authors: Amos Marc Bairoch, Rolf Apweiler, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the SWISS-PROT, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/SWISS-PROT, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

  • the swiss prot variant page and the modsnp database a resource for sequence and structure information on human protein variants
    Human Mutation, 2004
    Co-Authors: Yum Lina Yip, Alexandre Gattiker, Elisabeth Gasteiger, Holger Scheib, Alexander V Diemand, L Famiglietti, Amos Marc Bairoch
    Abstract:

    Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The SWISS-PROT protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the SWISS-PROT Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the SWISS-PROT knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly SWISS-PROT release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The SWISS-PROT variant pages are accessible from the NiceProt view of a SWISS-PROT entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP.

  • uniprot the universal protein knowledgebase
    Nucleic Acids Research, 2004
    Co-Authors: Rolf Apweiler, Amos Marc Bairoch, Elisabeth Gasteiger, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Hongzhan Huang, Rodrigo Lopez, Michele Magrane
    Abstract:

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the SWISS-PROT, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar SWISS-PROT (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

  • expasy the proteomics server for in depth protein knowledge and analysis
    Nucleic Acids Research, 2003
    Co-Authors: Elisabeth Gasteiger, Alexandre Gattiker, Ron D. Appel, Christine Hoogland, Ivan Ivanyi, Amos Marc Bairoch
    Abstract:

    The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.

  • expasy the proteomics server for in depth protein knowledge and analysis
    Nucleic Acids Research, 2003
    Co-Authors: Elisabeth Gasteiger, Alexandre Gattiker, Ron D. Appel, Christine Hoogland, Ivan Ivanyi, Amos Marc Bairoch
    Abstract:

    The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.

Henning Hermjakob - One of the best experts on this subject based on the ideXlab platform.

  • IntAct: an open source molecular interaction database
    Nucleic Acids Research, 2004
    Co-Authors: Henning Hermjakob
    Abstract:

    IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the SWISS-PROT team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.

  • intact an open source molecular interaction database
    Nucleic Acids Research, 2004
    Co-Authors: Henning Hermjakob, S. Kerrien, Luisa Montecchipalazzi, Chris Lewington, Sugath Mudali, Bernd Roechert, Sandra Orchard, Peter Roepstorff, Martin Vingron, Alfonso Valencia
    Abstract:

    IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains ∼2200 binary and complex interactions imported from the literature and curated in collaboration with the SWISS-PROT team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.

  • varsplic alternatively spliced protein sequences derived from swiss prot and trembl
    Bioinformatics, 2000
    Co-Authors: Paul Kersey, Henning Hermjakob, Rolf Apweiler
    Abstract:

    Summary: The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity searches. Availability: The program is available at ftp:// ftp.ebi. ac.uk/ pub/ software/ swissprot/ , together with regularly updated output files.

  • on the frequency of protein glycosylation as deduced from analysis of the swiss prot database
    Biochimica et Biophysica Acta, 1999
    Co-Authors: Rolf Apweiler, Henning Hermjakob, Nathan Sharon
    Abstract:

    Abstract The SWISS-PROT protein sequence data bank contains at present nearly 75 000 entries, almost two thirds of which include the potential N-glycosylation consensus sequence, or sequon, NXS/T (where X can be any amino acid but proline) and thus may be glycoproteins. The number of proteins filed as glycoproteins is however considerably smaller, 7942, of which 749 have been characterized with respect to the total number of their carbohydrate units and sites of attachment of the latter to the protein, as well as the nature of the carbohydrate-peptide linking group. Of these well characterized glycoproteins, about 90% carry either N-linked carbohydrate units alone or both N- and O-linked ones, attached at 1297 N-glycosylation sites (1.9 per glycoprotein molecule) and the rest are O-glycosylated only. Since the total number of sequons in the well characterized glycoproteins is 1968, their rate of occupancy is 2/3. Assuming that the same number of N-linked units and rate of sequon occupancy occur in all sequon containing proteins and that the proportion of solely O-glycosylated proteins (ca. 10%) will also be the same as among the well characterized ones, we conclude that the majority of sequon containing proteins will be found to be glycosylated and that more than half of all proteins are glycoproteins.

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