local alignment
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2022 ◽  
pp. 407-452
Author(s):  
Hamid D. Ismail
Keyword(s):  

2022 ◽  
pp. 1-47
Author(s):  
Mohammad Mohammadi ◽  
Peter Tino ◽  
Kerstin Bunte

Abstract The presence of manifolds is a common assumption in many applications, including astronomy and computer vision. For instance, in astronomy, low-dimensional stellar structures, such as streams, shells, and globular clusters, can be found in the neighborhood of big galaxies such as the Milky Way. Since these structures are often buried in very large data sets, an algorithm, which can not only recover the manifold but also remove the background noise (or outliers), is highly desirable. While other works try to recover manifolds either by pushing all points toward manifolds or by downsampling from dense regions, aiming to solve one of the problems, they generally fail to suppress the noise on manifolds and remove background noise simultaneously. Inspired by the collective behavior of biological ants in food-seeking process, we propose a new algorithm that employs several random walkers equipped with a local alignment measure to detect and denoise manifolds. During the walking process, the agents release pheromone on data points, which reinforces future movements. Over time the pheromone concentrates on the manifolds, while it fades in the background noise due to an evaporation procedure. We use the Markov chain (MC) framework to provide a theoretical analysis of the convergence of the algorithm and its performance. Moreover, an empirical analysis, based on synthetic and real-world data sets, is provided to demonstrate its applicability in different areas, such as improving the performance of t-distributed stochastic neighbor embedding (t-SNE) and spectral clustering using the underlying MC formulas, recovering astronomical low-dimensional structures, and improving the performance of the fast Parzen window density estimator.


2022 ◽  
Vol 32 (1) ◽  
Author(s):  
Amany M. Abd El Azim

Abstract Background Entomopathogenic nematodes (EPNs) are promising alternatives since they have many characteristics as a biological control agent against insect pests. Results Among indigenous EPN isolated, adapted to local environmental conditions by employing the Galleria baiting strategy, only one sample was positive for the presence of EPNs. The new isolate was identified at the species level using DNA sequencing of the internal transcribed spacer region and the Basic Local Alignment Search Tool search of GenBank showed that the isolate had a high similarity (99%) with that sequence available for Heterorhabditis taysearae. The pathogenicity of the EPN isolate was tested against the cotton leaf worm, Spodoptera littoralis (Boisd.) (Lepidoptera: Noctuidae), using different concentrations (60, 90, 120 and 150 IJs/larvae). Data showed that 150 IJs/larvae caused 100% mortality rate, followed by 120 IJs/larvae (90%), while 60 IJs/larvae showed the lowest rate (60%) after 72 h. Conclusions The present study indicated that the native isolate of EPN could be recommended against S. littoralis as an efficient tool in its control programs.


2022 ◽  
Vol 2022 ◽  
pp. 1-13
Author(s):  
Qiong Lou ◽  
Junfeng Li ◽  
Yaguan Qian ◽  
Anlin Sun ◽  
Fang Lu

RGB-infrared (RGB-IR) person reidentification is a challenge problem in computer vision due to the large crossmodality difference between RGB and IR images. Most traditional methods only carry out feature alignment, which ignores the uniqueness of modality differences and is difficult to eliminate the huge differences between RGB and IR. In this paper, a novel AGF network is proposed for RGB-IR re-ID task, which is based on the idea of global and local alignment. The AGF network distinguishes pedestrians in different modalities globally by combining pixel alignment and feature alignment and highlights more structure information of person locally by weighting channels with SE-ResNet-50, which has achieved ideal results. It consists of three modules, including alignGAN module ( A ), crossmodality paired-images generation module ( G ), and feature alignment module ( F ). First, at pixel level, the RGB images are converted into IR images through the pixel alignment strategy to directly reduce the crossmodality difference between RGB and IR images. Second, at feature level, crossmodality paired images are generated by exchanging the modality-specific features of RGB and IR images to perform global set-level and fine-grained instance-level alignment. Finally, the SE-ResNet-50 network is used to replace the commonly used ResNet-50 network. By automatically learning the importance of different channel features, it strengthens the ability of the network to extract more fine-grained structural information of person crossmodalities. Extensive experimental results conducted on SYSU-MM01 dataset demonstrate that the proposed method favorably outperforms state-of-the-art methods. In addition, we evaluate the performance of the proposed method on a stronger baseline, and the evaluation results show that a RGB-IR re-ID method will show better performance on a stronger baseline.


2022 ◽  
Vol 82 ◽  
Author(s):  
Z. Ahmad ◽  
M. H. Abbasi ◽  
S. R. Ahmad ◽  
N. Sheikh

Abstract Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.


2021 ◽  
Vol 34 (4) ◽  
Author(s):  
ENDANG WIJAYANTI ◽  
◽  
INDAH ISTIQOMAH ◽  
MURWANTOKO MURWANTOKO

The crustacean parasites are the most frequently encountered and cause significant economic loss in mariculture. These parasites infect fish fin, skin, gills, and buccal cavity. This study aims to describe copepod parasite in the buccal cavity of cultured groupers, Epinephelus spp., from Batam waters using morphological and molecular biology approaches. The tiger grouper, Epinephelus fuscoguttatus (Forsskal, 1775), and hybrid grouper, Epinephelus sp. showing lethargy and skin darkening were collected from sea cages. The parasite’s morphology was observed using light and scanning electron microscopes. The genomic DNA was isolated from the parasites and used as a template for amplification of cytochrome oxidase subunit-1 (Cox1) gene and followed by sequencing. The fish exhibited red nodules in the mouth cavity, on the lips, and gill arch in varying numbers and size of nodules. The copepodid, chalimus, and adult copepod stages were found from the nodule. Based on the presence of the oral cone, this parasite belonged to Siphonostomatoida order of copepods. Based on the structure of the caudal ramus with four long and four short setae, the first and second pair legs as biramous, and the third pair leg as uniramous, this parasite belonged to Pennellidae family of copepods. Basic local alignment search tool analysis of this Cox1 showed low homology within 80%, indicating that the DNA sequences of the parasite species were not reported in the GenBank. The unweighted pair group method using arithmetic average phylogenetic trees supported that this parasite belonged to the family Pennellidae. This is the first report on the pennellid parasite infection in the buccal cavity and gill arch of cultured groupers in Batam, Indonesia.


2021 ◽  
Vol 71 (6) ◽  
pp. 2091-94
Author(s):  
Ambreen Javed ◽  
Gulshan Ara Trali ◽  
Hassan Burair Abbas ◽  
Alia Sadiq

Objective: To predict the tertiary structure of human interferon alpha/beta receptor 2 protein. Study Design: Structure prediction by using bio informatics tools. Place and Duration of Study: Department of Biochemistry, Swat Medical College (STMC), Saidu Shareef, Swat, Pakistan, from Aug 2019 to Dec 2019. Methodology: All protein sequences of human interferon alpha/beta receptor 2 (isoforma, b and c) (IFNAR-2) were retrieved through the BLAST search (The Basic Local Alignment Search Tool) from available databases ‘NCBI’ (National Centre for Biotechnology Information) and ‘Uni Prot KB’ (The Universal Protein Resource). Sequence alignment was conducted by using Clustal Omega, to get the consensus sequence for IFNAR-2 protein. Consensus protein sequence of human IFNAR-2 was used for the prediction of the three-dimensional structure by employing Swiss-Model Server. Moreover, subcellular localization analysis was also performed by using CELLO2GO program. Results: Structural model of human IFNAR-2 protein was predicted and evaluated by Ramachandran dimension. Cellular localization of tertiary topological domains of the predicted models were revealed probability of localization of IFNAR-2 protein (isoform a, b & c) is highest in the plasma membrane due to the presence of the transmembrane alpha helical regions. Conclusion: This study predicted the tertiary structural dimensions of human IFNAR-2 protein, including the specific topological domains that contribute towards the subcellular compartmentalization and functional characteristics.


2021 ◽  
Vol 25 (9) ◽  
pp. 1637-1644
Author(s):  
B.A. Odogwu ◽  
J. Ukomadu ◽  
I. Igwe

The economic and medicinal important genus Jatropha contains many distinctly different species. To elucidate the genetic relationship of five common occurring Jatropha species namely J. multifida, J. podagrica, J.tanjorernsis, J. curcas, and J. gossypifolia, thirty-nine morphological, six phytochemical features and one arbitrary marker was used to screen and explore their similarity. Morphological data was obtained from the measurement of vegetative and reproductive parts while the presence of five phytochemicals was determined using differentphytochemical tests. The DNA of all five Jatropha species were amplified and sequenced using Ribolose 1, 5- biphosphate carboxylase molecular marker. The DNA sequences were then aligned using the Basic Local Alignment Search Tool for nucleotide 2.8.0 version of the National Center for Biotechnology Information database and phylogenetic trees were constructed using Paleontological Statistical software and Molecular Evolutionary Genetics Analysis version 7.0.26 software. From the results of the classical and phylogenetic cluster analysis, the five Jatropha species was separated into two major clusters. The highly distinctive J. gossypifolia was the only species that clustered separately from the other Jatropha species. Although, J. tanjorensis has been reported to be a hybrid from J. curcas and J. gossypifolia, the species did not segregate and cluster with these species, but segregated with J. multifida, and J.podagrica, indicating that this species is more closely related to J. multifida, and J. podagrica than J. curcas and J.gossypifolia. The result therefore provide information that would be useful in the plant improvement programs for the genus Jatropha.


2021 ◽  
Author(s):  
Mark J Cumming ◽  
Julien Gibon ◽  
Wayne S Sossin ◽  
Philip A Barker

Tumor necrosis factor receptors (TNFRs) regulate a diverse array of biological functions, including adaptive immunity, neurodevelopment, and many others. Although TNFRs are expressed in all metazoan phyla, a coherent model of the molecular origins of mammalian TNFRs—and how they relate to TNFRs in other phyla—has remained elusive. To address this, we executed a large-scale, systematic Basic Local Alignment Search Tool (BLAST)-based approach to trace the evolutionary ancestry of all 29 human TNFRs. We discovered that all human TNFRs are descendants of a single pre-bilaterian TNFR with strong sequence similarity to the p75 neurotrophin receptor (p75NTR), which we designate as PITA for ‘ p75NTR is the TNFR Ancestor’ . A distinct subset of human TNFRs—including EDAR, XEDAR and TROY—share a unique history as descendants of EDAR-XEDAR-TROY (EXT), which diverged from PITA in a bilaterian ancestor.  Most PITA descendants possess a death domain (DD) within their intracellular domain (ICD) but EXTs do not. PITA descendants are expressed in all bilaterian phyla and Cnidaria, but not in non-planulozoan ParaHoxozoa, suggesting that PITA originated in an ancestral planulozoan. Drosophila melanogaster TNFRs (Wengen (Wgn) and Grindelwald (Grnd)) were identified as divergent PITA descendants, providing the first evolutionary link between this model TNFR system and the mammalian TNFR superfamily. This study reveals PITA as the ancestor to human and Drosophila TNFR systems and describes an evolutionary model that will facilitate deciphering TNF-TNFR functions in health and disease.


2021 ◽  
Vol 119 (1) ◽  
pp. e2113075119
Author(s):  
Baoxing Song ◽  
Santiago Marco-Sola ◽  
Miquel Moreto ◽  
Lynn Johnson ◽  
Edward S. Buckler ◽  
...  

Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication–informed collinear anchor identification between genomes and performs base pair–resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor–binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.


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