How to use UniProt for comparative genomics?

Access UniProt Database

• Navigate to the UniProt website: www.uniprot.org. This is a comprehensive resource for protein sequence and functional information.

 

• Create a user account if necessary, to gain access to additional features like saving searches and creating personal datasets.

Search for Protein Sequences

• Utilize the search bar to find protein sequences of interest. You can search by protein name, gene name, or organism.

 

• Make use of UniProt's advanced search options to filter results based on specific criteria such as reviewed status, sequence length, or taxonomy.

Retrieve Protein Data

• Select the relevant protein entries from the search results to access detailed information, including sequence, structure, and functional annotations provided in the protein's UniProt entry.

 

• Download the protein sequences in FASTA format for further analysis. You can do this by selecting sequences and using the "Download" option.

Compare Sequences

• Use bioinformatics tools such as BLAST (Basic Local Alignment Search Tool) to compare your protein sequences. Many such tools are available on the UniProt site under the "Tools" section.

 

• Alternatively, download the sequences and use standalone software or web-based platforms like Clustal Omega or MUSCLE for multiple sequence alignments to identify conserved regions and assess evolutionary relationships.

Analyze Protein Features

• Leverage the annotated features provided by UniProt, such as domains, motifs, and post-translational modifications, to understand functional similarities and differences in a comparative context.

 

• Investigate protein function predictions, ontology terms, and biological roles provided in the UniProt entry to contextualize the comparative genomic findings.

Explore Cross-References and External Links

• Utilize the cross-references in UniProt entries to access additional data from related databases such as PDB for structural data, Ensembl for genomic context, or KEGG for pathways.

 

• Explore related literature and research articles linked in the UniProt entries to gain deeper insights and verify experimental findings in published studies.