De novo gene birth is the process by which new genes evolve from DNA sequences that
were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be …

There are several hundred million protein sequences, but the relationships among them are
not fully available from existing homolog detection methods. There is an essential need for …

The evolution of novel protein-coding genes from noncoding regions of the genome is one
of the most compelling pieces of evidence for genetic innovations in nature. One popular …

Evolutionary information is essential for the protein annotation. The number of homologs of a
protein retrieved is correlated with the annotations related to the protein structure or function …

Computational assignment of function to proteins with no known homologs is still an
unsolved problem. We have created a novel, function-based approach to protein annotation …

Recently developed protein language models have enabled a variety of applications of the
protein contextual embeddings. Per-protein representations (each protein is represented as …

Motivation Evolutionary information is crucial for the annotation of proteins in bioinformatics.
The amount of retrieved homologs often correlates with the quality of predicted protein …

Taxonomically restricted genes, or TRGs, are specific to a particular taxon that can be found
only in the genomes of single species or are represented as orthologs in closely related …

Multiple sequence alignment is a basic procedure in molecular biology, and it is often
treated as being essentially a solved computational problem. However, this is not so, and …

Nearly-exponential growth and heterogeneity of biological sequence data make the task of
biological sequence retrieval from databases more important and challenging than ever. In …