Protein Sequence Logos

Protein Sequence Logos visualizes aligned RNA and protein sequences as sequence and structure logos to quantify per-position information content and, for base-paired RNA, mutual information between paired bases.

Key Features:

• Schneider and Stephens (1990) foundation: Implements the sequence logo representation following Schneider and Stephens (1990).
• Incorporation of Prior Frequencies: Integrates prior frequencies of bases or amino acids to adjust information content calculations using background symbol distributions.
• Handling Gaps in Alignments: Accommodates gaps within alignments to represent insertions and deletions in evolutionary comparisons.
• Mutual Information Calculation: Calculates mutual information between paired bases for RNA alignments when base pairings are indicated.
• Structure Logos for Base-Paired Regions: Generates Structure Logos that display both sequence and structural information for base-paired RNA regions.
• Information Content Visualization: Represents each character height proportional to its frequency at a position, sorts characters from most to least frequent, and sets the total stack height to the information content measured in bits.

Scientific Applications:

• Consensus Sequence Determination: Determine consensus sequences by identifying the most prominent characters at each alignment position.
• Analysis of Sequence Variability: Highlight positions with high variability to identify potential sites of functional or evolutionary significance.
• Functional and Structural Insights: Use mutual information and structure logos to infer how sequence variation affects RNA structure and function.

Methodology:

Characters are stacked at each alignment position with heights proportional to symbol frequency and sorted from most to least common; the total stack height equals information content in bits, and mutual information is computed for annotated base-paired RNA positions.