LogoJS

LogoJS renders sequence logos to visualize consensus sequences and annotate positional features such as covalent nucleotide modifications, multi-nucleotide symbols, binding energy penalties, and neural network–derived negative weights.

Key Features:

• Sequence logo rendering: Renders sequence logos that represent consensus sequences and positional information content.
• Vector graphics output: Produces logos using vector graphics for scalable, high-fidelity visual representations.
• Covalent modification symbols: Supports symbols indicating covalent modifications on nucleotides at specific positions.
• Multi-letter representations: Supports multi-letter/multi-nucleotide symbols at each position to illustrate complex motif models.
• Below-axis extended symbols: Renders extended symbols below the x-axis to denote binding energy penalties or negative values.
• Neural network weight visualization: Represents negative weights from neural network outputs as positional logo elements.
• Implementation language: Implemented in plain JavaScript.

Scientific Applications:

• Consensus motif visualization: Visualizing nucleotide consensus sequences and positional information from alignments or motif models.
• Representation of covalent nucleotide modifications: Depicting positional occurrence of covalent modifications on nucleotides within motifs.
• Complex motif modeling: Illustrating models with multi-nucleotide features using multi-letter symbols per position.
• Binding energy and specificity depiction: Visualizing binding energy penalties and positional contributions to binding specificity.
• Neural network interpretation: Visualizing negative weights and positional contributions derived from neural network models.

Methodology:

Rendering sequence logos with vector graphics, supporting per-position multi-letter symbols, covalent-modification symbols, and extended below-axis symbols for binding energy penalties or neural-network-derived negative weights; implemented in plain JavaScript.