Skip to content

Instantly share code, notes, and snippets.

@pinbo

pinbo/SNP_primer_design.md

Created November 9, 2017 06:35
Show Gist options
  • Save pinbo/08569aea612b1aebf6df4a27cb540f6b to your computer and use it in GitHub Desktop.
Save pinbo/08569aea612b1aebf6df4a27cb540f6b to your computer and use it in GitHub Desktop.
Download ZIP
Some experiences for SNP primer design
Raw
SNP_primer_design.md
title subtitle author date
Primer Design Demo
with SNP_Primer_Design Tool
Junli Zhang
2017/11/11

background-image: url(https://upload.wikimedia.org/wikipedia/commons/9/96/Polymerase_chain_reaction.svg)

???

Image credit: Wikimedia Commons

Molecular Markers

Wikipedia's defination

In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome.

Types of molecular markers

  • RFLP: Restriction Fragment Length Polymorphism
  • RAPD: Random Amplified Polymorphic DNA
  • AFLP: Amplified Fragment Length Polymorphism
  • SSR: Simple Sequence Repeats
  • SNP: Single Nucleotide Polymorphism

Common PCR-based Genotyping Methods for SNP Analysis

  • CAPS:
    • Cleaved Amplified Polymorphic Sequences
    • A Single Nucleotide Polymorphism (SNP) where one allele creates (or removes) a naturally occurring restriction site
  • dCAPS:
    • Derived Cleaved Amplified Polymorphic Sequences
    • For SNPs that do not create a natural restriction site.
    • Uses mismatches in one PCR primer to create or remove a restriction site for one allele
  • KASP:
    • Kompetitive Allele Specific PCR

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment