SMAP effect-prediction

This is the manual for the SMAP effect-prediction module of the SMAP package.

SMAP effect-prediction is designed to provide biological interpretation of the haplotype call tables created by SMAP haplotype-window.

SMAP effect-prediction translates alternative haplotype sequences into their corresponding protein sequences for all haplotypes listed in the genotype call table created by SMAP haplotype-window, and thus identifies which alleles strongly affect protein-coding capacity.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Guidelines for SMAP effect-prediction
  • Required input
  • Commands & options
  • Example commands
  • Output
• Feature Description
  • Interpretation of the induced mutation spectrum in a plant collection
  • Concepts for “cleaning up”
• How It Works
  • Preparing input files with SMAP design and SMAP haplotype-window
  • The subsequent steps of SMAP effect-prediction
• Examples
  • Illustration of SMAP effect-prediction