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http://www.ebi.ac.uk/Tools/msa/kalign/

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

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http://www.ebi.ac.uk/ena/about/cram_toolkit

A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use.

Proper citation: CRAM (RRID:SCR_012975) Copy   

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http://phenomenal-h2020.eu/

Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.

Proper citation: PhenoMeNal (RRID:SCR_016605) Copy   

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http://www.ebi.ac.uk/Tools/maxsprout/

A database algorithm for generating protein backbone and side chain coordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.

Proper citation: MaxSprout (RRID:SCR_010687) Copy   

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http://purl.bioontology.org/ontology/GRO

Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).

Proper citation: Gene Regulation Ontology (RRID:SCR_010590) Copy   

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http://www.ebi.ac.uk/IPI

IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.

Proper citation: IPI (RRID:SCR_003012) Copy   

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http://www.ebi.ac.uk/ipd/

A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines.

Proper citation: IPD - Immuno Polymorphism Database (RRID:SCR_003004) Copy   

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http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

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http://www.ebi.ac.uk/intenz

IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

Proper citation: IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) Copy   

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http://ftp://ftp.ebi.ac.uk/pub/databases/taxonomy

The taxonomy database of the International Sequence Database Collaboration contains the names of all organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The database is available via the EBI SRS server of ftp.

Proper citation: Taxonomy (RRID:SCR_004299) Copy   

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http://www.ebi.ac.uk/thornton-srv/databases/sas/

SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be colored according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol. Use the form to identify your protein sequence of interest by: a) providing a PDB code, b) providing a UniProt code or accession number, c) pasting in your sequence, or d) uploading a PDB file. By default the whole PDB will be searched, but you can restrict the search using the Search Option box at the bottom.

Proper citation: SAS - Sequence Annotated by Structure (RRID:SCR_004635) Copy   

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http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+query+-libList+PATABS

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. Patent Abstracts is a set of biology-related abstracts of patent applications derived from data products of the European Patent Office (EPO). Patent documents from Europe (EP), USA (US) and World (WO) are included. Abstracts are extracted from the ESPACE ACCESS and GlobalPat CD/DVD products according to the International Patent Classification (IPC) classes covering biology topics. The data are transformed to a common XML format and combined into one SRS dataset.

Proper citation: Patent Abstracts (RRID:SCR_004839) Copy   

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http://www.ebi.ac.uk/uniprot/unisave/?help=0&session=

The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. Entries can be retrieved by entering a primary accession number or an entry name and pressing the Go! button. The result of the query is a list of entry versions with the UniProtKB database name, entry status, primary accession number, entry name, entry version, sequence version, release number and the release date, ordered by the release date, the latest version first. The entry version status can be ''''incorporated'''', ''''active'''', ''''changed'''', ''''replaced'''' or ''''deleted''''. An incorporated entry version is the first entry version added into UniProtKB, an active entry version is part of the latest public release, a changed entry version has been superseded by a newer entry version, a replaced entry has become secondary to another entry, and a deleted entry has been removed from the UniProtKB without becoming secondary to any other entry. For replaced entry versions, the status ''''Replaced'''' can be clicked to return all entries, which have the given entry as a secondary entry. If a date is provided as part of the query then only the version of the entry that was current at that date is displayed. Entries can be viewed by clicking ''''View'''' in the query results table. The ''''<< Earlier'''' and ''''Later >>'''' links can be used to access the earlier and later entry versions. The ''''Back to List'''' link returns the user to the query results table. Selecting ''''UniProtKB'''' or ''''Fasta'''' and pressing ''''Save'''' downloads the entry in flat file or fasta format. Comparison between entry versions is straightforward: selecting two entries and clicking the ''''Compare Selected'''' button will show the differences between the two entries. Whenever comparisons are made a Smith-Waterman sequence alignment is computed using SSEARCH, and displayed at the bottom of the entry. The actual alignment is displayed only when the sequences are not identical.

Proper citation: UniSave (RRID:SCR_004946) Copy   

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http://www-test.ebi.ac.uk/uniref/

Various non-redundant databases with different sequence identity cut-offs created by clustering closely similar sequences to yield a representative subset of sequences. In the UniRef90 and UniRef50 databases no pair of sequences in the representative set has >90% or >50% mutual sequence identity. The UniRef100 database presents identical sequences and sub-fragments as a single entry with protein IDs, sequences, bibliography, and links to protein databases. The two major objectives of UniRef are: (i) to facilitate sequence merging in UniProt, and (ii) to allow faster and more informative sequence similarity searches. Although the UniProt Knowledgebase is much less redundant than UniParc, it still contains a certain level of redundancy because it is not possible to use fully automatic merging without risking merging of similar sequences from different proteins. However, such automatic procedures are extremely useful in compiling the UniRef databases to obtain complete coverage of sequence space while hiding redundant sequences (but not their descriptions) from view. A high level of redundancy results in several problems, including slow database searches and long lists of similar or identical alignments that can obscure novel matches in the output. Thus, a more even sampling of sequence space is advantageous. You may access NREF via the FTP server.

Proper citation: UniRef at the EBI (RRID:SCR_004972) Copy   

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http://www.ebi.ac.uk/ebisearch/

The EB-eye Search system is developed on top of the Apache Lucene project framework, which is an Open-source, high-performance, full-featured text search engine library written entirely in Java. It uses this technology to index EBI databases in various formats (e.g. flatfiles, XML dumps, OBO format, etc.) and provides very fast access to the EBI''s data resources. The system allows the user to search globally across all EBI databases or individually in selected resources by using an Advance search.

Proper citation: EB-eye Search (RRID:SCR_006745) Copy   

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http://www.ebi.ac.uk/ipd/mhc

The IPD - MHC Database provides a centralized repository for sequences of the major histocompatibility complex from a number of different species. Through a number of international collaborations IPD is able to provide the MHC sequences of different species. The sequences provided by each group are curated by experts in the field and then submitted to the central database.

Proper citation: IPD-MHC- Major Histocompatibility Complex (RRID:SCR_007749) Copy   

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http://www.ebi.ac.uk/ipd/kir/

The IPD-KIR database provides a centralized repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily (IgSF) formerly called Killer-cell Inhibitory Receptors. They are composed of two or three Ig-domains, a transmembrane region and cytoplasmic tail which can in turn be short (activatory) or long (inhibitory). The Leukocyte Receptor Complex (LRC) which encodes KIR genes has been shown to be polymorphic, polygenic and complex like the MHC.

Proper citation: IPD-KIR - Killer-cell Immunoglobulin-like Receptors (RRID:SCR_007748) Copy   

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http://www.ebi.ac.uk/ipd/estdab/

The European Searchable Tumour Line Database (ESTDAB) Database and Cell Bank provide a service enabling investigators to search online for HLA typed, immunologically characterised tumour cells as part of the European Commission Fifth Framework Infrastructures Program. The following tools and pages are available in ESTDAB: :* Search ESTDAB on primary search determinants :* Search ESTDAB on all search determinants :* Dictionary of markers and techniques used

Proper citation: IPD-ESTDAB- The European Searchable Tumour Line Database (RRID:SCR_007746) Copy   

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http://www.mged.org/Workgroups/MAGE/mage.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems.

Proper citation: MAGE (RRID:SCR_002313) Copy   

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http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

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