Uniprot is a universal protein resource database that has been widely used by researchers for almost two decades. This article aims to provide an overview of the Uniprot database, including its history, structure, content, and functionalities. We will also showcase an example of how to use Uniprot in practice, highlighting its practical applications and benefits for researchers.
Table of Contents
- Introduction to Uniprot
- History of Uniprot
- Structure and Content of Uniprot
- The UniProtKB database
- The UniRef database
- The UniParc database
- Functionalities of Uniprot
- Sequence search
- Sequence analysis
- Data download
- Mapping and alignment
- Example of Using Uniprot in Practice
- Problem statement
- Solution using Uniprot
- Results and Interpretation
- Advantages of Using Uniprot
- Limitations of Using Uniprot
- Future Directions of Uniprot
Introduction to Uniprot
Uniprot, short for Universal Protein Resource, is a database that provides comprehensive information on proteins from different organisms, including humans, animals, plants, bacteria, and viruses. Uniprot is a collaborative project that involves several organizations, including the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR) in the United States. Uniprot aims to provide a centralized resource for protein sequence and functional information, enabling researchers to explore and analyze protein data in a user-friendly manner.
History of Uniprot
The Uniprot database was first released in 2002, merging two previously separate protein sequence databases: Swiss-Prot and TrEMBL. Swiss-Prot was a high-quality, manually curated protein sequence database that provided expert annotation and functional information on protein sequences. TrEMBL, on the other hand, was an automatically annotated protein sequence database that included all translations of the coding sequences present in the EMBL nucleotide sequence database. By combining these two databases, Uniprot aimed to provide a comprehensive and up-to-date resource of protein sequence and functional information.
Since its inception, Uniprot has undergone several updates and improvements. In 2007, the UniRef database was added to Uniprot, allowing the clustering of protein sequences at different levels of sequence identity. In 2012, the UniParc database was added to Uniprot, providing a unique and comprehensive archive of all publicly available protein sequences.
Structure and Content of Uniprot
The Uniprot database is divided into three main sections: the UniProtKB database, the UniRef database, and the UniParc database.
The UniProtKB database
The UniProtKB database is the main protein sequence database in Uniprot, containing high-quality, expert-curated protein sequences and functional information. The UniProtKB database contains three main sections:
- Swiss-Prot: This section contains expert-curated protein sequences and functional information, with a high level of manual annotation and integration of experimental data.
- TrEMBL: This section contains automatically annotated protein sequences, with functional information inferred from sequence analysis and homology-based transfer of annotation.
- UniProt Archive (UniParc): This section contains a comprehensive archive of all publicly available protein sequences, including redundant sequences, that have been reported in the literature or deposited in other sequence databases.
The UniRef database
Ref database is a clustered database that groups closely related protein sequences into clusters based on their sequence identity. UniRef clusters are created at three levels of sequence identity: UniRef100, UniRef90, and UniRef50. UniRef100 clusters contain the most similar sequences, while UniRef50 clusters contain the most divergent sequences. The UniRef database provides a condensed representation of the UniProtKB database, allowing for faster and more efficient searches.
The UniParc database
The UniParc database is a comprehensive archive of all publicly available protein sequences, including redundant sequences, that have been reported in the literature or deposited in other sequence databases. Each protein sequence in UniParc is assigned a unique identifier, allowing for easy tracking and cross-referencing of protein sequences across different databases.
Functionalities of Uniprot
Uniprot offers several functionalities that enable researchers to explore and analyze protein data in a user-friendly manner. Some of the key functionalities of Uniprot include:
Uniprot allows users to search for protein sequences using keywords, accession numbers, gene names, and other identifiers. Uniprot provides a powerful search engine that allows users to refine their search results based on several criteria, including organism, protein function, protein domain, and protein annotation.
Uniprot provides several tools for sequence analysis, including sequence alignment, motif search, and protein domain prediction. Uniprot also provides information on protein structure, including predicted secondary and tertiary structure, as well as information on protein-protein interactions and functional domains.
Uniprot allows users to download protein sequence and functional information in several formats, including FASTA, XML, and tab-delimited formats. Uniprot also provides several pre-formatted datasets for easy download and analysis, including the complete UniProtKB database and the UniRef clusters.
Mapping and alignment
Uniprot allows users to map and align protein sequences to other sequences or genomes, enabling the identification of homologous sequences and the detection of sequence variations. Uniprot also provides several tools for multiple sequence alignment and phylogenetic analysis.
Uniprot provides expert-curated protein annotation and functional information, including protein names, descriptions, and ontologies. Uniprot also allows users to contribute to the annotation of protein sequences, enabling the community to improve and expand the knowledge base of protein function and structure.
Example of Using Uniprot in Practice
To showcase the practical applications of Uniprot, let’s consider the following problem statement:
“I want to identify potential drug targets in the human proteome that are expressed in a tissue-specific manner and are involved in cancer progression.”
Solution using Uniprot
To solve this problem, we can use Uniprot to identify tissue-specific proteins that are known to be involved in cancer progression. Here’s how:
- Search for “human proteome” in Uniprot.
- Use the “Advanced Search” function in Uniprot to filter the search results based on tissue-specific expression patterns.
- Use the “Protein function” filter to identify proteins that are known to be involved in cancer progression.
- Use the “Sequence alignment” function in Uniprot to compare the identified proteins with known drug targets and identify potential drug candidates.
Results and Interpretation
Using Uniprot, we can identify several tissue-specific proteins that are known to be involved in cancer progression, including receptor tyrosine kinases (RTKs) and transcription factors. By comparing these proteins with known drug targets, we can identify several potential drug candidates that may be effective in treating cancer.
Advantages of Using Uniprot
Uniprot offers several advantages over other protein sequence databases, including:
Uniprot is a comprehensive database that covers all known protein sequences, including those from model organisms and non-model organisms. Uniprot also provides comprehensive functional information on each protein sequence, including protein names, descriptions, and ontologies.
Uniprot is expert-curated, meaning that all protein annotations and functional information are carefully reviewed and curated by a team of expert biocurators. This ensures that the information provided by Uniprot is accurate, reliable, and up-to-date.
Cross-referencing and integration
Uniprot integrates protein sequence and functional information from several different databases, including Gene Ontology (GO), InterPro, and Pfam. This allows for easy cross-referencing and integration of protein data across different databases.
Uniprot provides a user-friendly interface that allows researchers to easily search for and analyze protein data. Uniprot also provides several tools and resources for sequence analysis, annotation, and data download.
Uniprot is a valuable resource for researchers working in the field of protein science. Its comprehensive coverage, expert curation, and user-friendly interface make it an essential tool for protein sequence analysis and functional annotation. By using Uniprot, researchers can gain a deeper understanding of protein structure and function, and identify potential drug targets and therapeutic candidates.
- What is Uniprot?
Uniprot is a comprehensive database of protein sequences and functional information.
- What are the different databases that are integrated into Uniprot?
Uniprot integrates protein sequence and functional information from several different databases, including Gene Ontology (GO), InterPro, and Pfam.
- How is Uniprot different from other protein sequence databases?
Uniprot offers several advantages over other protein sequence databases, including comprehensive coverage, expert curation, and user-friendly interface.
- How can Uniprot be used in protein sequence analysis?
Uniprot can be used to search for protein sequences, analyze protein structure and function, and download protein data in several different formats.
- Can users contribute to the annotation of protein sequences in Uniprot?
Yes, Uniprot allows users to contribute to the annotation of protein sequences, enabling the community to improve and expand the knowledge base of protein function and structure.