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:
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
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.
Video Tip of the Week: Introduction to Biocuration and the career path: The ISB is a professional organization for biocurators At OpenHelix, we've long sung the praises of curators. Some of us have been curators and worked with curation and database development teams. All...
Video Tip of the Week: Complex Portal with Super Curators: From the same team that brings us the IntAct database for protein interaction data, the Complex Portal offers insights for additional levels of protein interactions that are organized around a biologic...
Friday SNPpets: This week's SNPpets illustrate that everyone's back in the saddle after the holidays with plenty of chatter. New and updated databases, tools, and other news abound. The financial threat to well known ...
Video Tip of the Week: UniProt updates, now including portable BED files: UniProt is one of the core resources that provides tremendously important curated information about proteins. You will find links to UniProt in lots of other tools and databases as well, but we've alwa...
Video Tip of the Week: RNACentral, wrangling non-coding RNA for simplifying access: Non-coding RNA data can be tricky to locate in public data sources. Sometimes it is handled with other gene sets, other times it's not. Some ncRNA may be found in databases of one type or one species, ...
Recent BioMed Central research articles citing this resource
Huang Kai-Yao et al., A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Systems Biology (2016) doi:10.1186/s12918-015-0244-1
Buffon P. Marjoriê et al., rs1888747 polymorphism in the FRMD3 gene, gene and protein expression: role in diabetic kidney disease. Diabetology Metabolic Syndrome (2016) doi:10.1186/s13098-015-0121-5
Mosquera-Rendón Jeanneth et al., Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2364-4
Zamboni Anita et al., Early transcriptomic response to Fe supply in Fe-deficient tomato plants is strongly influenced by the nature of the chelating agent Plant genomics. BMC Genomics (2016) doi:10.1186/s12864-015-2331-5
Lozano-Amado Daniela et al., Identification of repressive and active epigenetic marks and nuclear bodies in Entamoeba histolytica. Parasites Vectors (2016) doi:10.1186/s13071-016-1298-7