mmnashrullah/Primer_Blast_Multiple

Fork of ShuXingYu94's Primer Blast Multiple (https://github.com/ShuXingYu94/Primer_Blast_Multiple)

Primer_Blast_Multiple

Aim:

To carry out NCBI Primer-Blast-like function locally with unpublished genome database, and maybe for further use.

Current plans:

• Local blast with NCBI Blast+ through Biopython.
• Regular design of PCR primers and locally blast for specificity.
  ↘︎ Regardless of the position of the primers
• Design primers for qPCR in case of needing Exon junction span or Intron inclusion.
• Add a visualize function to visualize every primer pair's position on the given gene sequence with each use.
• While dealing with species like B. napus(2n = 4x = 38, AACC), each gene could have multiple copies(or homologous genes). For initial expression analysis, input multiple gene data and get consensus primers.
• For detecting SNP of the same gene of different cultivars(same species), design Allele-specific PCR primers.

Required environment:

1. Python3

2. NCBI Blast+

3. Database created with NCBI Blast+

4. Certain directory in order for outputting

5. Python Packages:

   • Biopython

   • os

   • Pandas

   • Primer3-py

Required parameters:

↘︎ Check Primer3 Documentation for detail

1. Email (in case of contact from NCBI)

2. Gene id, Database (to download sequence from NCBI GenBank)

   ↘︎NCBI efetch database

3. Output address, Database address (to save the result)

4. E-value, Identity (to check specificity)

Optimal parameters: (for designing primers)

1. Gene name (to name saved files)

2. Other parameters (for particular need in designing primers)