Spaced Seeds Research Articles

Computational Biomimetics of Winged Seeds

We develop a computational pipeline to facilitate the biomimetic design of winged seeds. Our approach leverages 3D scans of natural winged seeds to construct a bio-inspired design space by interpolating them with geodesic coordinates in the 3D diffeomorphism group. We formulate aerodynamic design tasks with probabilistic performance objectives and adapt a gradient-free optimizer to explore the design space and minimize the expectation of performance objectives efficiently and effectively. Our pipeline discovers novel winged seed designs that outperform natural counterparts in aerodynamic tasks, including long-distance dispersal and guided flight. We validate the physical fidelity of our pipeline by showcasing paper models of selected winged seeds in the design space and reporting their similar aerodynamic behaviors in simulation and reality.

An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matching

An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matching

Rodents mediate the relationship between seed rain, seed bank, and plant community with increased grazing disturbance.

Seed rain and the soil seed bank represent the dispersal of seeds in space and time, respectively, and can be important sources of recruitment of new individuals during plant community regeneration. However, the temporal dynamics of seed rain and the mechanisms by which the seed rain and soil seed bank may play a role in plant community regeneration with increased grazing disturbance remain unclear. Seed rain, soil seed bank, aboveground vegetation, and rodent density were sampled along a grazing gradient in an alpine marsh on the eastern Tibetan Plateau. We described the temporal dynamics of seed dispersal using Bayesian generalized mixed models, and nonmetric multidimensional scaling and the structural equation model were used to examine the effects of grazing disturbance on the relative role of seed rain and soil seed bank on aboveground plant community regeneration. The temporal dynamics of seed rain changed from a unimodal to a bimodal pattern with increased grazing disturbance. Both species diversity and seed density of the seed rain and seed bank increased significantly with increased grazing disturbance. Increased grazing disturbance indirectly increased the similarity of composition between seed rain, seed bank, and aboveground plant community by directly increasing species diversity and abundance of aboveground plant community. However, increased grazing disturbance also indirectly decreased the similarity of seed rain, soil seed bank, and aboveground plant community by directly increasing rodent density. The similarity between seed rain and aboveground plant community was greater than that of the soil seed bank and aboveground plant community with increased grazing disturbance. Grazing disturbance spreads the risk of seed germination and seedling establishment by changing the temporal dynamics of seed dispersal. Plants (positive) and rodents (negative) mediated the role of seed rain and soil seed bank in plant community regeneration. The role of seed rain in plant community regeneration is higher than the seed bank in disturbed alpine marshes. Our findings increase our understanding of the regeneration process of the plant community, and they provide valuable information for the conservation and restoration of alpine marsh ecosystems.

Coding genomes with gapped pattern graph convolutional network.

Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets. However, the highly variable lengths of genome sequences severely impair the presentation of sequences as input to the neural network. Genetic variations further complicate tasks that involve sequence comparison or alignment. Inspired by the theory and applications of "spaced seeds," we propose a graph representation of genome sequences called "gapped pattern graph." These graphs can be transformed through a Graph Convolutional Network to form lower-dimensional embeddings for downstream tasks. On the basis of the gapped pattern graphs, we implemented a neural network model and demonstrated its performance on diverse tasks involving microbe and mammalian genome data. Our method consistently outperformed all the other state-of-the-art methods across various metrics on all tasks, especially for the sequences with limited homology to the training data. In addition, our model was able to identify distinct gapped pattern signatures from the sequences. The framework is available at https://github.com/deepomicslab/GCNFrame.

Generating Images of Rare Concepts Using Pre-trained Diffusion Models

Text-to-image diffusion models can synthesize high quality images, but they have various limitations. Here we highlight a common failure mode of these models, namely, generating uncommon concepts and structured concepts like hand palms. We show that their limitation is partly due to the long-tail nature of their training data: web-crawled data sets are strongly unbalanced, causing models to under-represent concepts from the tail of the distribution. We characterize the effect of unbalanced training data on text-to-image models and offer a remedy. We show that rare concepts can be correctly generated by carefully selecting suitable generation seeds in the noise space, using a small reference set of images, a technique that we call SeedSelect. SeedSelect does not require retraining or finetuning the diffusion model. We assess the faithfulness, quality and diversity of SeedSelect in creating rare objects and generating complex formations like hand images, and find it consistently achieves superior performance. We further show the advantage of SeedSelect in semantic data augmentation. Generating semantically appropriate images can successfully improve performance in few-shot recognition benchmarks, for classes from the head and from the tail of the training data of diffusion models.

MISSH: Fast Hashing of Multiple Spaced Seeds.

Alignment-free analysis of sequences has revolutionized the high-throughput processing of sequencing data within numerous bioinformatics pipelines. Hashing k-mers represents a common function across various alignment-free applications, serving as a crucial tool for indexing, querying, and rapid similarity searching. More recently, spaced seeds, a specialized pattern that accommodates errors or mutations, have become a standard choice over traditional k-mers. Spaced seeds offer enhanced sensitivity in many applications when compared to k-mers. However, it's important to note that hashing spaced seeds significantly increases computational time. Furthermore, if multiple spaced seeds are employed, accuracy can be further improved, albeit at the expense of longer processing times. This paper addresses the challenge of efficiently hashing multiple spaced seeds. The proposed algorithms leverage the similarity of adjacent spaced seed hash values within an input sequence, allowing for the swift computation of subsequent hashes. Our experimental results, conducted across various tests, demonstrate a remarkable performance improvement over previously suggested algorithms, with potential speedups of up to 20 times. Additionally, we apply these efficient spaced seed hashing algorithms to a metagenomic application, specifically the classification of reads using Clark-S [Ounit and Lonardi, 2016]. Our findings reveal a substantial speedup, effectively mitigating the slowdown caused by the utilization of multiple spaced seeds.

Pengaruh Wadah dan Lama Penyimpanan Terhadap Viabilitas dan Vigor Benih Hotong (Setaria italica (L) Beauv)

The aim of this research is that hotong seeds can be preserved for a long time so that they can be stored and used for cultivation in the next planting season. This research was conducted at the Tissue Culture Laboratory and Plant Physiology Laboratory at the Faculty of Agriculture, Pattimura University, Ambon, which took place from February to May 2021. Completely randomized design method, two factors, three replications. The first factor was seeds in open space (A0), seeds in aluminum foil (A1), seeds in glass bottles (A2), seeds in clear plastic (A3), and seeds in white cloth (A4). Another factor is the retention time (B) which consists of three stages, namely: 1 month (B1), 2 months (B2), and 3 months (B3) storage. BNJ test and Anova analysis at 95% confidence level. The treatment to maintain the quality of the hotong seeds was the 3rd month storage aluminum foil (A3B3) which could maintain a moisture content of 9.4%, PTM 80.67%, and the growth rate and vigor of hotong seeds at 81%, and the worst treatment in maintaining the quality of viability and vigor. seeds were calico fabric treated in the 3rd month of storage (A1B3).

PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches

BackgroundTechnical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candidate positions within a reference sequence. We may create pairs (“position”, “subsequence”) for the reference sequence and keep all such records without compression, even on a budget computer. As sequences for new and reference genomes differ, the goal is to find anchors, so we tolerate differences and keep the number of candidate positions with the same anchors to a minimum. Spaced seeds (masks ignoring symbols at specific locations) are a way to approach the task. An ideal (full sensitivity) spaced seed should enable us to find all such positions subject to a given maximum number of mismatches permitted.ResultsSeveral algorithms to assist seed generation are presented. The first one finds all permitted spaced seeds iteratively. We observe specific patterns for the seeds of the highest weight. There are often periodic seeds with a simple relation between block size, length of the seed and read. The second algorithm produces blocks for periodic seeds for blocks of up to 50 symbols and up to nine mismatches. The third algorithm uses those lists to find spaced seeds for reads of an arbitrary length. Finally, we apply seeds to a real dataset and compare results for other popular seeds.ConclusionsPerFSeeB approach helps to significantly reduce the number of reads’ possible alignment positions for a known number of mismatches. Lists of long, high-weight spaced seeds are available in Additional file 1. The seeds are best in weight compared to seeds from other papers and can usually be applied to shorter reads. Codes for all algorithms and periodic blocks can be found at https://github.com/vtman/PerFSeeB.

Effects of spaced k-mers on alignment-free genotyping.

Alignment-free, k-mer based genotyping methods are a fast alternative to alignment-based methods and are particularly well suited for genotyping larger cohorts. The sensitivity of algorithms, that work with k-mers, can be increased by using spaced seeds, however, the application of spaced seeds in k-mer based genotyping methods has not been researched yet. We add a spaced seeds functionality to the genotyping software PanGenie and use it to calculate genotypes. This significantly improves sensitivity and F-score when genotyping SNPs, indels, and structural variants on reads with low (5×) and high (30×) coverage. Improvements are greater than what could be achieved by just increasing the length of contiguous k-mers. Effect sizes are particularly large for low coverage data. If applications implement effective algorithms for hashing of spaced k-mers, spaced k-mers have the potential to become an useful technique in k-mer based genotyping. The source code of our proposed tool MaskedPanGenie is openly available on https://github.com/hhaentze/MaskedPangenie.

Theoretical aspects of the increase in the efficiency of sowing grain crops in resource-saving technologies

The paper presents theoretical studies of the aspects of increasing efficiency of sowing during the implementation of resource-saving technologies, which allow determining the speed of the seed at any time of its movement along the curvilinear section of the distributor and at the moment it leaves the surface of the distributor. The main factors influencing the distance and trajectory of the flight of seeds, taking into account the arch of the under-shoulder space, were identified. Graphical dependences of the flight distance of the seed on its speed when leaving the distributor surface, on the angle of the seed descent from the distributor and on the installation height of the seed distributor above the soil surface were plotted. The analysis of dependences allowed concluding that in order to obtain the greatest flight distance of seeds in the under-shoulder space, it is necessary to have the maximum installation height of the seed distributor and the speed of the seeds when leaving its surface. The angle of descent of seeds from the curved part of the distributor should tend to zero with the horizontal axis, subject to the condition of the absence of their impacts on the internal elements of a coulter. These graphic dependencies allow determining the numerical values of the specified parameters for blade coulters with different design characteristics.

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Purpose. Determination of technical and technological parameters of the electrotechnological means for presowing disinfection and stimulation of seeds in the electric field depending from the coefficient of distribution of seeds of crops on the surface of the precipitating rotating electrode. Methods. Analytical and calculation method using the structural and technological parameters of the working area of the means for pre-sowing disinfection and stimulation of seeds in an electric field and the data on the physical and mechanical properties of crop seeds. Results. A prototype of an electrotechnological device for pre-sowing disinfection and stimulation of crop seeds by a complex of electrophysical actions has been developed. The main condition for effective disinfection of seeds on the surface of a disk electrode in a high voltage electric field is the turning of the grains in the working space of the electrode system and their uniform distribution by the thickness of the grains in one layer on the surface of the rotating depositing electrode. This movement of the seed masses on the moving electrode ensures uniform treatment of each grain, which increases the efficiency of the process of disinfection of seed and grain material. To implement the process of pre-sowing disinfection and stimulation of seeds in an electric field, a structural and technological scheme of seed feeding and distribution in the working area of the electrode space of the device was developed Analytical dependences of feeding, expected productivity, and design parameters of the device scrapers on the coefficient of distribution of crop seeds on the surface of the depositing rotating electrode were obtained. They allow us to establish what the seed supply to the surface of the depositing electrode should be, and, accordingly, the performance of the prototype and the parameters of the scraper system to ensure the turning of the seeds in space and their uniform distribution by the thickness of the seeds in one layer on the surface of the rotating depositing electrode. Conclusions 1. The dependence of the supply of crop seeds to the surface of the electrode in terms of the expected productivity of the plant on the coefficient of seed distribution kz in the working area of processing was established. The distribution of seeds on the electrode surface in terms of specific gravity depends on the supply of seeds to the disk, the height and length of the scrapers. Uniform distribution of wheat, soybeans, corn, sunflower seeds on the surface of the disk in a single layer is achieved when kz = 1. In this case, the seed supply to the disk is in the range of 0.3–0.6 kg/s. 2. The parameters of the scraper system in terms of the length and height of the three scrapers depended on the type of crop seeds and their supply to the working area of the electrode system. The length of the first scraper for different seeds was in the range of values 229–246 mm, height – 18–24 mm; the second – 164–181 mm and 36–47 mm; the third - 83–132 mm and 54–71 mm, respectively. The specific weight of seeds on the surface of the disk is 1.3–3.7 kg/m2. The expected productivity of the prototype of the electrotechnological means for seeds of agricultural crops will be in the range of 0.7–2.1 t/h. Keywords: seed distribution coefficient, scraper system, seed disinfection, electric field, productivity, feeding, electrotechnological installation, pathogenic microflora, molds

ЭКсперимент по выращиванию «космической» ели сизой в дендрарии Главного ботанического сада имени Н.В. Цицина Российской академии наук

The interest in studying the possibilities of introduction of Picea glauca (Moench.) Voss. into the territory of the center of the European part of the Russian Federation is explained by a wide range of ecological characteristics of this species, as well as by the prospects of its use in various spheres of the country’s economy. The article deals with the results of a unique experiment to study the growth peculiarities of the grey-blue spruce trees, which were grown from seeds that had been in Earth orbit during the Soviet-American space flight of the Soyuz‑19 and Apollo spacecrafts in July 1975. The seeds were sown in May 1976 and in 1983 the seedlings were planted in the exposition of Arboretum. During the following years, these plants were continuously monitored – tree decline and their condition were recorded. At the age of 40 years, measurements of diameters and heights were made. It was noted that trees grown from “space” seeds had significantly higher growth rates in height and diameter by the age of 40 than the control, with spruce from seeds that had been to space exceeding the control in diameter by 1 cm and in height by 3 m. However, trees grown from “space” seeds had a predominance of weak condition plants, with 17% more plants than the control, and a 38% higher dieback than the control. This can be interpreted as a distant consequence of the effects of stresses produced by experimental seeds in space.

Extraction of long k-mers using spaced seeds.

The extraction of k-mers from reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These methods tend to be more accurate when the used k-mers are unique in the analyzed DNA, and thus the use of longer k-mers is preferred. When the read lengths of short read sequencing technologies increase, the error rate will become the determining factor for the largest possible value of k. Here we propose LoMeX which uses spaced seeds to extract long k-mers accurately even in the presence of sequencing errors. Our experiments show that LoMeX can extract long k-mers from current Illumina reads with a similar or higher recall than a standard k-mer counting tool. Furthermore, our experiments on simulated data show that when the read length further increases enabling even longer k-mers, the performance of standard k-mer counters declines, whereas LoMeX still extracts long k-mers successfully.

Contributions to the Mathematical Modeling of the Threshing and Separation Process in An Axial Flow Combine

The paper presents a mathematical model that characterizes the process of threshing and separation from the threshing machine with an axial flow of a thresher, taking into account the following input parameters: material flow, rotor speed, distance between rotor and counter rotor, mean density of processed material, feed speed, length of thresher and separating surface. Output parameters, such as the distribution function of separated seeds, distribution density function of separated seeds and distribution function of free seeds in the threshing space, as well as the distribution function of unthreshed seeds, together with the value of evacuation losses, were used to control the modeling process.

NtHash2: recursive spaced seed hashing for nucleotide sequences.

MotivationSpaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.ResultsntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism.Availability and implementationntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.Supplementary information Supplementary data are available at Bioinformatics online.

Global, highly specific and fast filtering of alignment seeds

BackgroundAn important initial phase of arguably most homology search and alignment methods such as required for genome alignments is seed finding. The seed finding step is crucial to curb the runtime as potential alignments are restricted to and anchored at the sequence position pairs that constitute the seed. To identify seeds, it is good practice to use sets of spaced seed patterns, a method that locally compares two sequences and requires exact matches at certain positions only.ResultsWe introduce a new method for filtering alignment seeds that we call geometric hashing. Geometric hashing achieves a high specificity by combining non-local information from different seeds using a simple hash function that only requires a constant and small amount of additional time per spaced seed. Geometric hashing was tested on the task of finding homologous positions in the coding regions of human and mouse genome sequences. Thereby, the number of false positives was decreased about million-fold over sets of spaced seeds while maintaining a very high sensitivity.ConclusionsAn additional geometric hashing filtering phase could improve the run-time, accuracy or both of programs for various homology-search-and-align tasks.

The Effect of Genotypes and plant distances on leaf miner infestation in pea plant (Pisum sativum L.)

Green pea plants are liable to infestation by vegetable leaf miner Liriomyza spp. (Diptera: Agromyzidae) ,is a polyphagous species spread around the world, becoming vegetable crop pests. An experiment was carried out in the directory of agricultural research, Iraq, Sulaimanyah in Plant Protection Research Station in Bakrajo region during season 2020 to study the effect of different genotypes and planting spaces on the population density of Leaf miner infesting pea plants. The obtained results revealed that the population density of leaf miner on pea plants not differed significantly according to the planting spaces (5cm, 15cm and 25cm) during the season. Planting of pea seeds in the planting space (5cm) population density of leaf miner decreased by the first planting space (%16.895). The pea plants were sown in the planting space (15cm) infested by the highest level of the insect (leaf miner) (%18.452) followed by pea plants sowing at the planting space (25cm) which infestation level was (%17.967) respectively. for the physical characters of the plant (plant high, total weight and weight of 100 grains) the results shows that the sowing pea in the spacing of (15cm) were significantly difference, followed by (5cm) while planting distance of (25cm) showed lowest levels of result for last three parameters.

Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data.

A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related Rmaps can be used to correct errors in Rmap data, and to find overlaps between Rmaps to assemble consensus optical maps. Previous Rmap overlap aligners are computationally very expensive and do not scale to large eukaryotic data sets. We present Selkie, an Rmap overlap aligner based on a spaced (l,k)-mer index which was pioneered in the Rmap error correction tool Elmeri. Here we present a space efficient version of the index which is twice as fast as prior art while using just a quarter of the memory on a human data set. Moreover, our index can be used for filtering candidates for Rmap overlap computation, whereas Elmeri used the index only for error correction of Rmaps. By combining our filtering of Rmaps with the exhaustive, but highly accurate, algorithm of Valouev et al. (2006), Selkie maintains or increases the accuracy of finding overlapping Rmaps on a bacterial dataset while being at least four times faster. Furthermore, for finding overlaps in a human dataset, Selkie is up to two orders of magnitude faster than previous methods.

Design and rationale for parametres of the seed-fertilizer seeder coulter for subsoil broadcast seeding

For sowing grain crops on stubble, stubble seeders with tine coulters are used, which perform technological operations in one pass. However, they do not meet the requirements of the agricultural machinery to ensure an even distribution of seeds in the sub-spear space. The subsoil no-drill planting creates the most favorable conditions for growth and development of cultivated crops and at the same time, grain crop yields are increased on average by 10…30%. Using no-drill planting, seeders equipped with spear coulters with spreaders for no-drill subsoil seeding provide the best quality and distribute the seeds evenly over the field. The article proposes the original design of the seed drill coulter for no-drill planting, which provides an even seed distribution over the feeding area. As a result of the theoretical researches the optimal parameters of the diffuser for the grain drill coulter are determined and the dependence between the unevenness on the test parameters of the diffuser and the height of the pendulum spreader, the base diameter are obtained. The purpose of this research is to develop the design and rationale of parameters of the grain drill for subsoil no-drill planting, the use of which will reduce the uneven distribution of grain crops seeds or mineral fertilizer granules.

Analysis of the process of pneumatic conveying of seeds through the seed drill tube

This paper presents the methodology and results of experimental studies of the dependence of the flight distance of seeds in the sub-coulter space on the speed of airflow, provides a comparative analysis of theoretical and experimental studies. The experiment results in determination of mathematical expectation of seed flight distance, mean square deviation, coefficient of variation, absolute and relative errors. The resulting function is linear in nature and shows a directly proportional relationship of factors. For the quantitative evaluation of compliance of theoretical and experimental studies, the authors chose the following criteria: correlation coefficient r, Fisher criterion F and Student coefficient t. Calculations results in the following values: r=0.535; tp=1.031; Fp=3.493. Comparative analysis of theoretical and experimental studies shows that dependencies have an average force relationship (r=0.535), the difference between them is not significant (tT ≻ tP ), and the proposed model is adequate (FT ≻ FP ).