Pests of mustard_Identification_Management_Dr.UPR.pdf
Automated and manual Primer designing and its validation using Bioinformatics tools by Zarlish attique
1. Name: Zarlish Attique
Roll no: 187104
BS: Bioinformatics
Semester: 5th
Subject: Applications of Bioinformatics
Teacher: Sajid Dilzak Khan
Date:08-03-2020
Government Post Graduate College Mandian Abbottabad
Power point slides created by Zarlish Attique
Tools use for Manual and Automated Primer designing
ِيم ِحٰٱلر ِن همْحٰٱلر ِ هٰ
ٱَّلل ِمْسِب
2. Primer Specifications
1. Primer Length- greater 18 to 30 Nucleotides.
2. Melting temperature for Forward and reverse primer for hybridization and extension should
be controlled.
3. No Primer Dimer Formation.
4. Guanine Cytosine Content limit.
5. Runs and Repeats in the primer sequence.
6. Distance between Forward and reverse primer should be controlled.
7. No secondary structure formation.
3. Manual Methods for Primer Designing
1. NCBI: nucleotide database.
2. Pick gene of interest.
3. Perform BLASTn.
4. Select the Sequences.
5. Perform Multiple Sequence Alignment.
6. Find out Conserved Regions.
7. Take them as candidate sequences.
8. Open JustBio Register yourself.
9. Necessary Calculations.
10. Primer is ready to use!
