Background Multiple genome alignment remains a challenging problem. Effects of
recombination including rearrangement, segmental duplication, gain, and loss can create a …

k-mer-based methods are widely used in bioinformatics for various types of sequence
comparisons. However, a single mutation will mutate k consecutive k-mers and make most k …

String matching has been an extensively studied research domain in the past two decades
due to its various applications in the fields of text, image, signal, and speech processing. As …

Motivation: The next generation sequencing technologies are generating billions of short
reads daily. Resequencing and personalized medicine need much faster software to map …

With recent advances in next-generation sequencing (NGS) technology, large volumes of
data have been produced in the form of short reads. Sequence assembly involves using …

Motivation: The explosion of next-generation sequencing data has spawned the design of
new algorithms and software tools to provide efficient map** for different read lengths and …

New DNA sequencing technologies have achieved breakthroughs in throughput, at the
expense of higher error rates. The primary way of interpreting biological sequences is via …

We consider a new construction of locality-sensitive hash functions for Hamming space that
is covering in the sense that is it guaranteed to produce a collision for every pair of vectors …

We propose a general approach to compute the seed sensitivity, that can be applied to
different definitions of seeds. It treats separately three components of the seed sensitivity …

Biomolecular sequence comparison is the origin of bioinformatics. Today, powerful
sequence comparison methods, together with comprehensive biological databases, have …