The development of medical applications of machine learning has required manual
annotation of data, often by medical experts. Yet, the availability of large-scale unannotated …

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions
between parental genomes in a polyploid nucleus, frequently involving subgenome …

Background Tools for accurately clustering biological sequences are among the most
important tools in computational biology. Two pioneering tools for clustering sequences are …

The encounter of large amounts of biological sequence data generated during the last
decades and the algorithmic and hardware improvements have offered the possibility to …

Woody bamboos (Bambusoideae) are renowned for its polyploidy and rare flowering.
Bambusa odashimae is one of the bamboo species with the highest chromosome count …

Alignment-based methods have faced disadvantages in sequence comparison and
phylogeny reconstruction due to their high computational complexity. Alignment-free …

Traditional supervised learning methods applied to DNA sequence taxonomic classification
rely on the labor-intensive and time-consuming step of labelling the primary DNA …

Collagen is the most ubiquitous protein in the animal kingdom and one of the most abundant
proteins on Earth. Despite having a relatively repetitive amino acid sequence motif that …

Current tools for estimating the substitution distance between two related sequences
struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as …

Plant genomes include large numbers of transposable elements. One particular type of
these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using …