Bioinformatics has revolutionized our understanding of different proteins and their functions and UniProt is at the forefront of this field.
In the world of Bioinformatics, UniProt is a freely accessible and powerful tool that provides comprehensive information about protein sequence and function annotation. Along with serving as a hub of protein sequence data for protein analysis, UniProt enables us to cross-reference to other biological databases, making it one of the most valuable resources in research of Proteomics, Bioinformatics, Molecular Biology, and other related fields.
Here we will demonstrate the effective use of UniProt software to extract valuable biological insights whether you are a novice or a seasoned scientist.
What is UniProt?
UniProt (Universal Protein Resource) is a protein sequence and function information database that provides information about protein structure, function, interactions, and biological role. It has four key components;
UniProtKB is a core or central hub of UniProt and is divided into two sections:
Swiss-Prot: It features manually reviewed protein entries for high-quality and detailed functional annotations.
TrEMBL: It contains computationally predicted protein entries or sequences that are not manually reviewed
UniRef groups similar protein sequences in the form of clustered sets to reduce redundancy and speed up sequence analysis.
UniParc is a database of all publicly available protein sequences for preserving data and historical tracking.
It provides information of proteins of species whose genome have been sequenced.
Why use UniProt?
- UniProt offers several features that help us to have an efficient dry lab protein analysis:
- It helps user to get deeper insights to protein structure and interaction analysis.
- You can perform functional analysis through links to external resources.
- Performs efficient and accurate sequence alignment and comparison of similar proteins.
- UniProt cross-references with many other databases like Ensembl and PDB (Protein Data Bank).
- It has a user-friendly interface thus enabling easy search and navigation
Steps to Use UniProt:
To begin using Uniprot, open the official UniProt website in your browser, a well-organized website having a major search box will appear before you where you can input whatever protein you are searching for. you can search a protein name, gene, or keyword in the main search box and UniProt’s robust search engine will present relevant results to you.
For basic search, type a protein, gene, or organism in the search box. For example, if you are searching for IL6 or p53 protein type “IL6” or “p53” and press Enter. You will see a list of proteins matching your search.
For more specific queries, click on the “Advance” button next to the search bar. This will allow you to have refined research using filters like organism, subcellular localization, reviewed or unreviewed and more detailed attributes like sequence length or molecular weight of protein.
The key details in search results include:
- Accession Number: a unique identifier number for each protein.
- Protein Name: It’s the official name of the protein.
- Gene Name: It is the gene encoding that protein.
- Organism: The protein’s source organism.
For each search result, you will see reviewed Swiss-Prot and Unreviewed TrEMBL entries. If you are looking for highly reliable and curated information then focus on SwissProt entries.
Once, you click on a specific protein entry from the result you will be taken to a detailed information page having different sections like:
- Function describes the biological role and function of the protein.
- Subcellular Location, indicates the location of protein within the specific part of the cell.
- Names and Taxonomy, provide information about alternative protein names and organism classification.
- Disease and variants, provide information about disease caused by variants of desired gene.
- Post-Translational Modifications (PTMs), inform about modifications like phosphorylation.
- Protein-protein interaction, provides information on known or predicted interactions of the protein with other proteins.
- 3D Structure, links to external sources like PDB to explore 3D structures of protein.
- Family and Domains, inform about the family of proteins to which the desired protein is related based on sequence similarities
- The Similar proteins section provides information about proteins that are similar to the protein you searched
- Sequence and Isoform section displays the sequence and different isoforms of the desired protein.
For further analysis, you can download protein sequences by clicking on the “Download” button on protein entry page. For this purpose, you can choose different formats like FASTA for sequenced data and XML for annotations and structural data. These files can be used in other bioinformatics tools for further research. You can also export large datasets from UniProt in the form of spreadsheets in CSV or Excel format.
Tools from UniProt
UniProt offers several built-in bioinformatics tools like:
- BLAST: this software compares proteins against UniProt’s database for finding homologous proteins.
- Align: Aligns multiple protein sequences to study similarities and evolutionary relationships between them.
- Peptide Search: it identifies peptides by matching them to sequences using mass spectrometry data.
- Retrieve/ ID Mapping: for mapping ID between UniProt and other external databases and retrieving UniProt entries in batch.
These steps will help you to navigate UniProt’s website with ease and search for different proteins more efficiently.
Start exploring UniProt today to unlock valuable biological insights!
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