Searching and Navigating UniProt Databases

Sangya Pundir1, Michele Magrane1, Maria J. Martin1, Claire O'Donovan1, null null2

1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL‐EBI), Cambridge, 2 Protein Information Resource, Washington D.C.
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.27
DOI:  10.1002/0471250953.bi0127s50
Online Posting Date:  June, 2015
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Abstract

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. It provides ten searchable datasets and three main tools. The key UniProt datasets are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), the UniProt Archive (UniParc), and protein sets for completely sequenced genomes (Proteomes). Other supporting datasets include information about proteins that is present in UniProtKB protein entries such as literature citations, taxonomy, and subcellular locations, among others. This paper focuses on how to use UniProt datasets. The basic protocol describes navigation and searching mechanisms for the UniProt datasets, while two alternative protocols build on the basic protocol to describe advanced search and query building. © 2015 by John Wiley & Sons, Inc.

Keywords: UniProt; search; navigation; tutorial

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching UniProt Datasets
  • Basic Protocol 2: Advanced Search and Query Building
  • Basic Protocol 3: Adding Parameters Using Advanced Search
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Searching UniProt Datasets

  Necessary Resources
  • An up‐to‐date Web browser

Basic Protocol 2: Advanced Search and Query Building

  Necessary Resources
  • An up‐to‐date Web browser

Basic Protocol 3: Adding Parameters Using Advanced Search

  Necessary Resources
  • An up‐to‐date Web browser
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Figures

Videos

Literature Cited

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