Version Compatibility

Reference examples tested with: ggseqlogo 0.2 (CRAN; per Wagih 2017), Logomaker 0.8+ (Python), WebLogo 3.7+ (CLI), Biopython 1.83+ (motif parsing), MEME suite 5.5+.

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Sequence Logos

"Plot a sequence motif" -> Render a per-position stack of letters whose total height encodes information content (Schneider-Stephens 1990 Nucleic Acids Res 18:6097) and individual letter height is proportional to base/aa frequency. The information-content encoding makes conserved positions visually tall and variable positions visually short — the visual is the conservation profile.

• R: ggseqlogo::ggseqlogo (Wagih 2017 Bioinformatics 33:3645)
• Python: logomaker.Logo
• CLI: weblogo (Crooks 2004 Genome Res 14:1188)

The Single Most Important Modern Insight -- Bits vs Probability Are Different Visualizations