Transposable elements (TEs) are genomic units able to move within the genome of virtually
all organisms. Due to their natural repetitive numbers and their high structural diversity, the …

The production of genome sequences has led to another important advance in their
annotation, which is closely linked to the exact determination of their content in terms of …

Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a
long string is a central subproblem in many applications, including genome assembly, error …

As genomes evolve, they undergo large-scale evolutionary processes that present a
challenge to sequence comparison not posed by short sequences. Recombination causes …

Most genomes are populated by hundreds of thousands of sequences originated from
mobile elements. On the one hand, these sequences present a real challenge in the process …

Reproducible and target-specific polymerase chain reaction (PCR) amplification relies on
several interrelated factors of which primer design is central. Here, we describe new free …

Motivation: Matches to repetitive sequences are usually undesirable in the output of DNA
database searches. Repetitive sequences need not be matched to a query, if they can be …

Background The challenges of accurate gene prediction and enumeration are further
aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet …

The rapid development of high-throughput sequencing technologies means that hundreds of
gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools …

Motivation: Repetitive DNA sequences, besides having a variety of regulatory functions, are
one of the principal causes of genomic instability. Understanding their origin and evolution is …