UniProt Tools

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

1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL‐EBI), Wellcome Trust Genome Campus, Cambridge, 2 Protein Information Resource, University of Delaware, Newark, Delaware
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.29
DOI:  10.1002/0471250953.bi0129s53
Online Posting Date:  March, 2016
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Abstract

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the ‘BLAST’ tool for sequence similarity searching, the ‘Align’ tool for multiple sequence alignment, and the ‘Retrieve/ID Mapping’ tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa. This unit provides three basic protocols, three alternate protocols, and two support protocols for using UniProt tools. © 2016 by John Wiley & Sons, Inc.

Keywords: UniProt; search; navigation; tutorial

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Basic Local Alignment Search Tool in UniProt
  • Alternate Protocol 1: Basic Local Alignment Search Tool Through UniProt Text Search Results Pages
  • Support Protocol 1: Basic Local Alignment Search Tool Through UniProt Basket
  • Basic Protocol 2: Multiple Sequence Alignment in UniProt
  • Alternate Protocol 2: Align Tool Through UniProt Results Pages and Entry Pages
  • Support Protocol 2: Align Through UniProt Basket
  • Basic Protocol 3: Batch Retrieval and Id Mapping in UniProt
  • Alternate Protocol 3: Retrieve/Id Mapping Tool Through UniProt Basket
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Basic Local Alignment Search Tool in UniProt

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Alternate Protocol 1: Basic Local Alignment Search Tool Through UniProt Text Search Results Pages

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Support Protocol 1: Basic Local Alignment Search Tool Through UniProt Basket

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Basic Protocol 2: Multiple Sequence Alignment in UniProt

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Alternate Protocol 2: Align Tool Through UniProt Results Pages and Entry Pages

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Support Protocol 2: Align Through UniProt Basket

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Basic Protocol 3: Batch Retrieval and Id Mapping in UniProt

  Necessary Resources
  • A computer with an up‐to‐date Web browser

Alternate Protocol 3: Retrieve/Id Mapping Tool Through UniProt Basket

  Necessary Resources
  • A computer with an up‐to‐date Web browser
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PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
  Huang, H., McGarvey, P.B., Suzek, B.E., Mazumder, R., Zhang, J., Chen, Y., and Wu, C. H. 2011. A comprehensive protein‐centric ID mapping service for molecular data integration. Bioinformatics 27:1190‐1191. doi: 10.1093/bioinformatics/btr101.
  Ladunga, I. 2009. Finding homologs in amino acid sequences using network blast searches. Curr. Protoc. Bioinformatics 25:3.4:3.4.1‐3.4.34. doi: 10.1002/0471250953.bi0304s25.
  Simossis, V., Kleinjung, J., and Heringa, J. 2003. An overview of multiple sequence alignment. Curr. Protoc. Bioinformatics 3.7:3.7.1‐3.7.26. doi: 10.1002/0471250953.bi0307s03.
  UniProt Consortium, 2015. UniProt: A hub for protein information. Nucleic Acids Res. 43:D204‐D212. doi: 10.1093/nar/gku989.
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