BTW

BTW computes time-warping distances and Boltzmann-derived alignment probabilities between gene expression time series to identify temporally similar expression patterns and infer potential functional relationships.

Key Features:

• Dynamic Time Warping (DTW): Leverages Dynamic Time Warping (DTW), a quadratic-time algorithm, to compute smallest distances and optimal alignments between numerical sequences of differing lengths.
• Symmetric algorithm: Implements a recently developed symmetric algorithm that computes pairwise time-warping distances and the Boltzmann partition function.
• Boltzmann pair probabilities: Outputs Boltzmann pair probabilities that quantify the positional significance of positions within optimal time-warping alignments.
• Pairwise comparisons: Computes time-warping distances between each gene in file A and each gene in file B.
• Input format handling: Accepts two tab-separated text files containing gene expression time series that may have different numbers of time intervals with varying durations.
• Robustness to length differences: Accommodates sequences of differing lengths, providing flexibility relative to Euclidean distance and correlation coefficient comparisons.
• Identification of temporal similarity: Detects genes with similar temporal expression patterns that can imply related biological functions.

Scientific Applications:

• Gene expression comparison: Comparing gene expression time series to identify temporally similar genes across conditions or experiments.
• Function inference: Inferring potential related biological functions from similar temporal expression patterns.
• Cross-sampling alignment: Aligning expression profiles across datasets with differing numbers of time intervals and varying durations to study gene expression dynamics.

Methodology:

Computes DTW-based optimal alignments and time-warping distances, applies a symmetric algorithm to obtain the Boltzmann partition function, and derives Boltzmann pair probabilities for pairwise comparisons between genes in the two tab-separated input files.