Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the...

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets. We then perform an analysis of seeds built over those alphabet and compare t...

The ability of seeds to germinate at high salt concentration in the soil is crucial importance for the survival and perpetuation of many plant species. Therefore, we examined effects of different concentrations of NaCl (200, 400, 600 and 800 mM) on germination of four species from fam. Solanaceae and Brassicaceae (Capsicum annum, Solanum lycopersicum, Brasica oleracea and Sinapis alba). By this...

—Many studies have examined seed removal by rodents without regard to possible biases from inadvertent olfactory cues left by the researcher. I compared removal rates of seeds that had direct contact with human skin (scent treatment) with those that had no direct contact (no-scent treatment). Seeds of two species were alternated at 5 m intervals along a straight transect in a native grassland i...

Dynamic dosimetry is becoming the standard to evaluate the quality of radioactive implants during brachytherapy. It is essential to obtain a 3D visualization of the implanted seeds and their relative position to the prostate. For this, a robust and precise segmentation of the seeds in 2D X-ray is required. First, implanted seeds are segmented using a region-based implicit active contour approac...

Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2-8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation sign...

Pseudoperonospora cubensis, an obligate biotrophic oomycete causing devastating foliar disease in species of the Cucurbitaceae family, was never reported in seeds or transmitted by seeds. We now show that P. cubensis occurs in fruits and seeds of downy mildew-infected plants but not in fruits or seeds of healthy plants. About 6.7% of the fruits collected during 2012-2014 have developed downy mi...

Seeds are complex structures that unite diploid maternal tissues with filial tissues that may be haploid (gametophyte), diploid (embryo), or triploid (endosperm). Maternal tissues are predicted to favor smaller seeds than are favored by filial tissues, and filial genes of maternal origin are predicted to favor smaller seeds than are favored by filial genes of paternal origin. Consistent with th...

A machine vision system was developed to inspect the quality of rice seeds. Five varieties of Jinyou402, Shanyou10, Zhongyou207, Jiayou and IIyou were evaluated. The images of both sides of rice seed with black background and white background were acquired with the image processing system for identifying external features of rice seeds. Five image sets consisting of 600 original images each wer...

The e#ect of +/h, -**ppm calcium hypochlorite soaking on microbial quality of mung seeds and sprouts was investigated. The extended chlorine soaking did not completely eliminate the microflora of the seeds but significantly reduced microbial proliferation rates during storage. Generally, microbial counts of the chlorine-soaked seeds were significantly lower than that of the control. Total plate...