Rambutan tree (Nepheliumlappaceum L.) is an important but a lesser known fruit tree in Ghana and has several nutritional and medicinal uses. Efforts to establish plantation of Rambutan in Ghana to ensure its sustainable use is challenged with unavailable planting materials because the seeds are recalcitrant in nature, loses viability easily when exposed to dryness. Seeds are therefore sown dire...

Standard search techniques for DNA repeats start by identifying seeds, that is, small matching words, that may inhabit larger repeats. Recent innovations in seed structure have led to the development of spaced seeds [8] and indel seeds [9] which are more sensitive than contiguous seeds (also known as k-mers, k-tuples, l-words, etc.). Evaluating seed sensitivity requires 1) specifying a homology...

In order to quantify the response of birds to experimental manipulations of seed availability and densities of granivorous rodents and ants, we counted granivorous birds and measured diurnal and nocturnal seed removal on 24 plots during winter months in the Chihuahuan Desert. Removal of single, widely spaced millet seeds provided a reliable measure of bird and rodent foraging activity. Avian fo...

Spaced seed is a filter method invented to efficiently identify the regions of interest in similarity searches. It is now well known that certain spaced seeds hit (detect) a randomly sampled similarity region with higher probabilities than the others. Assume each position of the similarity region is identity with probability p independently. The seed optimization problem seeks for the optimal s...

rambutan tree (nepheliumlappaceum l.) is an important but a lesser known fruit tree in ghana and has several nutritional and medicinal uses. efforts to establish plantation of rambutan in ghana to ensure its sustainable use is challenged with unavailable planting materials because the seeds are recalcitrant in nature, loses viability easily when exposed to dryness. seeds are therefore sown dire...

Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...

A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related can be used to correct errors Rmap data, and find overlaps between assemble consensus maps. Previous overlap aligners are computationally very expensive do not scale large eukaryotic sets. We present Selkie , an aligner based on a spaced <i...

Sequence similarity search is a fundamental way of analyzing nucleotide sequences. Despite decades of research, this is not a solved problem because there exist many similarities that are not found by current methods. Search methods are typically based on a seed-and-extend approach, which has many variants (e.g. spaced seeds, transition seeds), and it remains unclear how to optimize this approa...

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns....