This document provides instructions for designing primers for gene identification. It outlines steps to select a gene from a viral genome, search for the gene on NCBI, select sequences in FASTA format, perform a multiple sequence alignment on Clustal Omega, choose a sequence with the fewest mutations, and design primers for it using Primer 3 Plus while adjusting parameters for size, melting temperature, GC content, and product size. The summary concludes by asking if there are any questions.

1. LAB # 04:
PRIMER
DESIGNING
(IDENTIFICAT
ION OF
GENE)
TODAY’S TOPIC

2. Select a
gene from
your viral
genome
Press Search
Select Nucleotide from list
Put Put gene name in NCBI search bar
• use proper spellings
Go Go to NCBI at
https://www.ncbi.nlm.nih.gov/
Searc
h
Gene name

5. Sequence selection
Select at least 5 sequences
• Open word file and paste sequences in FASTA format
Go to Clustal Omega at
https://www.ebi.ac.uk/Tools/msa/clustalo/
• Select DNA
• Put all sequences in box
• Submit
Result
Select sequence with least mutations

7. SELECTED A
GENE
SEQUENCE
Now take sequence
in FASTA
And go to PRIMER 3
PLUS

8. Primer 3 plus
Go to webpage at https://www.primer3plus.com/
Put sequence in box
Adjust parameters
• Primer size = 18-22
• Tm = 55-65
• GC % = 40-80
• Product size = 150-350
Select pick primers

14. It was easy,
wasn’t it?
ANY
QUESTIONS?
??
FEEL FREE
TO ASK