Skylign

Skylign generates sequence logos that visualize positional conservation and residue frequencies from sequence alignments and profile hidden Markov models (HMMs) to support interpretation of conservation and functional constraints.

Key Features:

• Unified framework: Generates logos from both sequence alignments and profile hidden Markov models (HMMs), ensuring consistent representation across these data types.
• Logo representation: Uses stacked-letter logos where stack height reflects positional conservation and individual letter heights indicate residue or nucleotide frequencies.
• Interactive output: Produces interactive logo plots that expose underlying numerical values for positions and symbols.
• Bias mitigation: Mitigates sampling bias by down-weighting redundant sequences and integrating observed counts with informed priors.
• Gap parameter depiction: Simplifies the depiction of gap parameters within logos to represent insertions and deletions.
• Conservation scaling options: Provides options to scale letter heights using alternative calculations of positional conservation.

Scientific Applications:

• Sequence conservation analysis: Visualizes and quantifies conservation patterns in nucleotide and protein alignments and profile HMMs.
• Functional and structural inference: Supports interpretation of functional constraints and hypothesis generation related to gene function and protein structure.
• Evolutionary analysis: Aids interpretation of evolutionary relationships and constraints across aligned sequences.

Methodology:

Generates logos from sequence alignments and profile HMMs; constructs stacked-letter representations with stack heights reflecting positional conservation and letter heights reflecting observed frequencies; down-weights redundant sequences and integrates observed counts with informed priors; simplifies depiction of gap parameters; offers alternative positional-conservation scaling and produces interactive plots exposing underlying numerical values.