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uniprot application

by Mr. Jermain Becker MD Published 4 years ago Updated 3 years ago

What is UniProt?

10/04/2018 · UniProt provides several application programming interfaces (APIs) to query and access its data programmatically: UniProt website REST API. What: RESTful URLs that can be bookmarked, linked and used in programs for all entries, queries and tools available through this website. Data is available in all formats provided on the website, e.g. text, XML, RDF, FASTA, …

What are the API's available in UniProt?

UniProt provides several application programming interfaces (APIs) to query and access its data programmatically. 1. RESTful UniProt website What: RESTful URLs that can be bookmarked, linked and used in programs for all entries, queries and tools available through the UniProt website. Data is available in all formats provided on the website, e.g. text, XML, RDF, FASTA, …

How can I download data from UniProt?

UniProt Consortium is formed in 2002, which is collaboration between European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). By means of computational analysis, and sequence archiving, this consortium functions in manual curation of protein sequences of interest and develop a user-friendly web platform that …

What formats are available for UniProtKB data?

22/11/2021 · The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation …

What is the use of UniProt?

UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation.

How do I run UniProt?

BLAST sequence similarity searching.BLAST results.Aligning multiple protein sequences.Alignment results.Batch retrieval & ID mapping.Converting UniProt identifiers to external identifers (or vice versa)Mapping results.Peptide search.More items...

What are the important features of UniProt?

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

What type of knowledge database is UniProt?

protein sequence databaseUniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.22-Nov-2021

How reliable is UniProt?

UniProtKB encompasses several individual protein sequence resources that are depicted on this page. If you are talking about a sequence that is from SwissProt (manually reviewed/curated sequences) or UniRef100 clusters then that sequence is likely perfectly accurate.26-Oct-2018

How many protein sequences are in UniProt?

UniProtKB/Swiss-Prot has curated over 81 000 variants in 13,000 human protein sequence records from peer-reviewed literature, annotated with information on the functional impact and clinical significance, when known.25-Nov-2020

How many sequences are in UniProt?

INTRODUCTION Release 2021_04 of 29-Sep-2021 of UniProtKB/TrEMBL contains 225013025 sequence entries, comprising 78379501201 amino acids. 12728037 sequences have been added since release 2021_03, the sequence data of 31110 existing entries has been updated and the annotations of 93040713 entries have been revised.

What is a UniProt ID?

The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the proteome. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome. UniProtKB entries can be linked to one or more UPIDs.10-Apr-2018

What are the stages of UniProt database?

This process consists of 6 major mandatory steps: (1) sequence curation, (2) sequence analysis, (3) literature curation, (4) family-based curation, (5) evidence attribution, (6) quality assurance and integration of completed entries.10-Apr-2018

Is Swiss-Prot and UniProt same?

Swiss-Prot (created in 1986) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. UniProtKB/Swiss-Prot is now the reviewed section of the UniProt Knowledgebase.10-Apr-2018

Is UniProt primary or secondary database?

Many data resources have both primary and secondary characteristics. For example, UniProt accepts primary sequences derived from peptide sequencing experiments.

How can I download protein structure from UniProt?

Retrieving sequences from the websitePerform your favorite query and view the resulting list of entries (e.g. this query retrieves all UniProtKB entries that are part of the human proteome: proteome:UP000005640)Click the Download button in the query result page.More items...•26-Jan-2021

Funding

  • UniProt is supported by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute on Aging (NIA), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIG…
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Past Funding

  • UniProt has been supported by the NIH grants U01HG02712 (2002-2010) and U41HG006104 (2010-2014). UniProt activities at EMBL-EBI have benefited from the FP7 SLING project (2009-2012, contract number 226073), British Heart Foundation grants SP/07/007/23671 and RG/13/5/30112, the Parkinson's Disease United Kingdom GO grant G-1307 and the NIH GO grant …
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Further Information

Contact The Uniprot Consortium Members

  • European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Phone: (+44 1223) 494 444 Fax: (+44 1223) 494 468 SIB Swiss Institute of Bioinformatics Centre Medical Universitaire 1, rue Michel Servet 1211 Geneva 4 Switzerland Phone: (+41 22) 379 50 50 Fax: (+41 22) 379 58 58 Protein Information Resource (P…
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How to Cite Us

  • If you find UniProt useful, please consider citing our latest publication: The UniProt Consortium UniProt: the universal protein knowledgebase in 2021 Nucleic Acids Res. 49:D1 (2021) ...or choose the publication that best covers the UniProt aspects or components you used in your work:
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2019

  • The UniProt Consortium UniProt: a worldwide hub of protein knowledge Nucleic Acids Res. 47:D506-515 (2019) Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A, UniProt Consortium. Enzyme annotation in UniProtKB using Rhea Bioinformatics 36(6):1896-1…
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2018

  • The UniProt Consortium UniProt: the universal protein knowledgebase Nucleic Acids Res. 46:2699 (2018) Pichler K, Warner K, Magrane M, UniProt Consortium SPIN: Submitting Sequences Determined at Protein Level to UniProt Curr. Protoc. Bioinformatics 62(1):e52 (2018)
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2017

  • The UniProt Consortium UniProt: the universal protein knowledgebase Nucleic Acids Res. 45:D158-D169 (2017) Chen C, Huang H, Wu CH. Protein Bioinformatics Databases and Resources Methods Mol. Biol. 1558:3-39 (2017) Ding R, Boutet E, Lieberherr D, Schneider M, Tognolli M, Wu CH, Vijay-Shanker K, Arighi CN. eGenPub, a text mining system for extending computationally m…
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2016

  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View Methods Mol. Biol. 1374:23-54 (2016) Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium The …
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2015

  • Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Rios D, O'Donovan C, Vizcaino JA, Martin MJ. Analysis of the tryptic search space in UniProt databases Proteomics 15:48-57 (2015) Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step toward…
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2014

  • Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation. Hum. Mutat. 35:927-935 (2014) Huntley RP, Sawford T, Martin MJ, O'Donovan C. Understanding how and why the Gene Ontology and its annotations evolve: th…
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2013

  • Chen C, Li Z, Huang H, Suzek BE, Wu CH; UniProt Consortium A fast Peptide Match service for UniProt Knowledgebase Bioinformatics 29:2808-2809 (2013) Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Martin MJ, O'Donovan C, Apweiler R. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans Database (Oxford) bas…
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2012

  • Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios I, Gaudet P. Biocurators and Biocuration: surveying the 21st century challenges Database (Oxford) (2012) Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra …
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2011

  • Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. The impact of focused Gene Ontology curation of specific mammalian systems Plos One (2011) Burmester A, Shelest E, Glockner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuer…
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    • select * from `nova_menu_menu_items` where `nova_menu_menu_items`.`parent_id` in (1) order by `order` asc
      240μs/vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35receivinghelpdeskask
      Metadata
      Backtrace
      • 24. /vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35
      • 25. /vendor/outl1ne/nova-menu-builder/src/helpers.php:33
      • 27. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 28. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 29. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
    • select `id`, `post_title`, `slug` from `posts` where `status` = 'publish' and `posts`.`deleted_at` is null order by RAND() limit 10
      1.54s/app/View/Composers/SidebarView.php:22receivinghelpdeskask
      Metadata
      Bindings
      • 0. publish
      Backtrace
      • 14. /app/View/Composers/SidebarView.php:22
      • 15. /app/View/Composers/SidebarView.php:12
      • 16. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:124
      • 17. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:162
      • 20. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:177
    • select * from `fake_users` where `fake_users`.`id` = 48628 limit 1
      680μsview::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15receivinghelpdeskask
      Metadata
      Bindings
      • 0. 48628
      Backtrace
      • 21. view::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15
      • 23. /vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:108
      • 24. /vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 25. /vendor/livewire/livewire/src/ComponentConcerns/RendersLivewireComponents.php:69
      • 26. /vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:61
    App\Models\FakeUser
    1
    Outl1ne\MenuBuilder\Models\MenuItem
    1
    Outl1ne\MenuBuilder\Models\Menu
    1
    App\Models\JsonPostContent
    1
    App\Models\Post
    11
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        _previous
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        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /uniprot-application
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
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        request_server
        0 of 0
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