Primer DesignPrimer DesignPrimer DesignPrimer Design

1. Gene Runner

2. Oligo 6

4. Manual

3. Primer 3(on line)

Gene Runner1.Sequence Insertion

Oligo 6

Manual1. Reference sequence & other sequences (NCBI)

2. Alignment (Mega 4)

3. Sequence selection (In selected gene)

4. Blast (NCBI)

5. TM (oligo analyzer, oligo6, gene runner)

6. Secondary structures (loop, hairpin,…)

7. False priming (oligo 6)

HCVGenome

Alignment

Current oligo length

Position number

Non specific band

- Length-Miss match *5-7nt from 3’ end