Learn to use the UniProt Knowledgebase, which has detailed curated information about known proteins, with predictions and computational assignments for both characterized and uncharacterized proteins. The UniRef layer provides clustered handy links to related proteins. UniParc archive records collect non-redundant but complete collections of protein sequence data. This tutorial will explore each type of record--UniProt, UniRef, and UniParc, and examine available search strategies. This resource is a foundational tool for proteomics research.

You will learn:

  • to perform text searches for relevant protein information
  • to search with sequences as a starting point
  • to understand the different types of UniProt records
  • to create multi-sequence alignments from protein records using Clustal
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Advanced Analysis and Queries. You might find the other tutorials in the group interesting:

BioMart: Management and querying of many types of biological data

DBTSS: Database of Transcriptional Start Sites

ENCODE Data at UCSC: ENCODE Data at UCSC

Galaxy: Analysis tools for researchers


This tutorial is a part of the tutorial group Protein-centric and protein structure resources. You might find the other tutorials in the group interesting:

Pfam: Protein Domain families

RCSB PDB: RCSB Protein Data Bank

MMDB: Molecular Modeling Database at NCBI

Entrez Protein: NCBI's Entrez Protein for amino acid-centric information

Structural Biology Knowledgebase: The Protein Structure Initiative Structural Biology Knowledgebase

CATEGORIES

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

BLOG POSTS

What's The Answer? (proteins without genes in the dbs): This week's highlighted discussion offers a peek at some odd situations in public databases. Sometimes there are things missing that you can't quite figure out. I thought the exploration of why this ha...

Video Tip of the Week: Aquaria, streamlined access to protein structures for biologists: This week's Video Tip of the Week is Aquaria, a new resource for exploring protein structures, mutations, and similarities to other proteins. It's a very well-designed and interactive experience for en...

Video Tip of the Week: PhosphoSitePlus, protein post-translational modifications : Nucleotide sequence data and analysis commands the bulk of my attention on most days. But certainly post-translational modification of proteins has a lot of influence on the ultimate function (or dysfu...

Bioinformatics tools extracted from a typical mammalian genome project [supplement]: This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to ...

Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Son Minky et al., Structural importance of the C-terminal region in pig aldo-keto reductase family 1 member C1 and their effects on enzymatic activity. BMC Structural Biology (2015) doi:10.1186/s12900-014-0028-7

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Nguyen Van-Nui et al., Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Bioinformatics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Bioinformatics (2015) doi:10.1186/1471-2105-16-S1-S1

Gopalakrishnan Subramaniam et al., The extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum Streptomyces sp. in chickpea. SpringerPlus (2015) doi:10.1186/s40064-015-0811-3

AraĆ­nga Mariluz et al., Opposing regulation of endolysosomal pathways by long-acting nanoformulated antiretroviral therapy and HIV-1 in human macrophages. Retrovirology (2015) doi:10.1186/s12977-014-0133-5