Retrieval of nucleotide or protein sequence data from the Entrez database of NCBI.

 

Aim of the Experiment

To retrieve nucleotide or protein sequence data from the Entrez database of NCBI.

Principle

Entrez is an integrated search and retrieval system developed by NCBI that allows users to access biological databases such as nucleotide, protein, genome, and literature.

It works by:

• Accepting search queries (gene name, organism, accession number)
• Retrieving relevant records
• Providing sequence data in formats like FASTA and GenBank

 Requirements

• Computer with internet connection
• Web browser
• Access to NCBI

Step-by-Step Procedure

Step 1: Open NCBI Website

• Go to: NCBI
• You will see the Entrez search bar at the top

Step 2: Select Database

• Click the dropdown menu beside the search bar
• Choose:
  • Nucleotide (for DNA/RNA sequences)
  • Protein (for amino acid sequences)

Step 3: Enter Search Query

• Type relevant keywords:
  • Gene name (e.g., BRCA1)
  • Organism name (e.g., Homo sapiens)
  • Accession number (if known)

Example:
BRCA1 Homo sapiens

Step 4: Run Search

• Click Search
• A list of results will appear

Step 5: Apply Filters (Optional)

• Use filters on the left panel:
  • Organism
  • Sequence length
  • Molecule type

Step 6: Select a Record

• Click on a suitable entry
• Ensure it matches:
  • Correct organism
  • Complete sequence (if required)

Step 7: View Sequence Details

• The record page shows:
  • Gene information
  • Accession number
  • Sequence length
  • Features (CDS, exons, etc.)

Step 8: Retrieve Sequence in FASTA Format

• Click FASTA (top of the record)
• Sequence will appear in FASTA format:

>Sequence_ID Description
ATGCGTACGTAGCTAGCTAG...

Step 9: Download the Sequence

• Click Send to → File
• Choose format: FASTA
• Click Create File
• Save to your computer

Step 10: Record the Data

• Note in practical file:
  • Gene name
  • Organism
  • Accession number
  • Sequence length

Result

Successfully retrieved DNA/protein sequence from Entrez in FASTA format.

Precautions

• Use correct spelling of gene and organism
• Verify accession number
• Select reviewed/validated sequences
• Avoid partial sequences unless required

Applications

• Primer designing
• Sequence alignment
• Phylogenetic analysis
• Gene annotation
• Protein structure prediction

Viva Voce Questions (with Answers)

1. What is Entrez?
   A database retrieval system of NCBI.
2. What is an accession number?
   A unique identifier for a sequence record.
3. What is FASTA format?
   A text format for representing nucleotide/protein sequences.
4. Which database is used for DNA sequences?
   Nucleotide database.
5. Which database is used for protein sequences?
   Protein database.
6. What is GenBank?
   A public database of nucleotide sequences.
7. Why is filtering important?
   To obtain accurate and relevant results.
8. Can Entrez retrieve protein sequences?
   Yes.