Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping

Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they have a direct impact on predicted protein annotations.

We developed a discriminative, alignment-free algorithm for homology detection with quasi-linear complexity, enabling theoretically much faster homology searches. To reach this goal, we convert the protein sequence into numeric biophysical representations. These are shrunk to a fixed length using a novel vector quantization method which uses a Discrete Cosine Transform compression. We then compute, for each compressed representation, similarity scores between proteins with the Dynamic Time Warping algorithm and we feed them into a Random Forest. The WARP performances are comparable with state of the art methods.

The method is available at http://ibsquare.be/warp.

Supplementary data are available at Bioinformatics online.