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1,199 results for “Alignement”
Multiple sequence alignment of DNA-A sequences from ACMBFV, ACMV, CMMGV, EACMCV, EACMKV, EACMMV, EACMV, EACMZV, SACMV, ICMV, SLCMV (11 species)
<p>All full-length DNA-A sequences available in GenBank as of July 2019 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were manually adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p>
Supplementary material 2 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S2 – Python script for custom grid search of hyperparameters for optimization of the neural network
Supplementary material 3 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S3 – The parameters utilized in the grid search for each of the five machine learning algorithms tested in the design of the Alfie package
Supplementary material 4 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S4 – Jupyter notebook with tutorial demonstrating how to apply the Alfie classifier in the Python programming language, and how to train custom alignment-free classifiers using the Alfie training module
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
<p><span>Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of <i>Streptococcus suis</i>, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of <i>S. suis</i>). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.</span></p>
Duration of tooth alignment with fixed appliances: a with meta-analysis
<p>Datasets for all analyses</p>
Coregonus spp. opsin amplicon sequence alignments
<p>Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus <i>Coregonus</i>) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were sequenced for individuals of <i>C. artedi</i>,<i> C. hoyi</i>,<i> C. kiyi</i>, and <i>C. zenithicus.</i> Comparisons revealed species-specific differences in a key spectral tuning amino acid in <i>rhodopsin</i> (Tyr261Phe substitution), suggesting local adaptation of <i>C. kiyi </i>to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.</p>
Multilevel Text Alignment with Cross-Document Attention
<p>This benchmark belongs to our EMNLP2020 paper: <a href="https://arxiv.org/abs/2010.01263">Multilevel Text Alignment with Cross-Document Attention</a>.</p>
Prosopis laevigata microsatellite and sequence alignment data
<p>Patterns of genetic and phylogeographic structure and recent population history of plant species in the Mexican arid zones has been scarcely investigated. <i>Prosopis laevigata</i> is the most widely spread species of mesquite in Mexico, with extensive populations in the arid and semi-arid zones of the central and northern plateaus and scattered presence in southern Mexico. We evaluated the genetic and phylogeographic structure of this species to infer its recent demographic history. We genotyped six nuclear microsatellite loci and sequenced the psbA3´-trnH chloroplast DNA (cpDNA) region in individuals from 21 populations covering the whole distribution of the species. Nuclear genetic diversity was moderately high (H<sub>E</sub>=0.527) and genetic differentiation was moderate (F<sub>ST</sub>=0.16). A positive correlation between genetic diversity and latitude was observed. The cpDNA analyses indicated a lack of phylogeographic structure in <i>P. laevigata</i> (G<sub>ST</sub>=0.090, N<sub>ST</sub>=0.101; P=0.497). Historical demography statistics indicated a population expansion supported by a skyline plot analysis, the star-like shape of the haplotype network, and the unimodal shape of the mismatch distribution. Ecological niche modeling suggested a contracted distribution into west-central Mexico during the Last Interglacial (~140 Ka), followed by an expansion in both northwards and southwards directions in the Last Glacial Maximum (~22 Ka), which continued in the mid-Holocene (~6 Ka) and the present. Results are congruent with a recent population growth and colonization of newly opened arid zones by <i>P. laevigata</i> populations. This pattern is consistent with the high capacity of colonization of nutrient-poor areas, high germination rates and resistance to drought reported for <i>Prosopis</i> species</p>
Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
<p class="BodyA"><span><b>Background:</b> The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus <i>Hibiscus </i>L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. <i>Hibiscus </i>is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested three alternative scenarios describing different polyploidization events.</span></p> <p class="BodyA"><span><b>Results:</b> Using target sequence capture, we designed a new probe set for <i>Hibiscus </i>and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of <i>Hibiscus</i> sampled shared one genome duplication with <i>H. syriacus</i> and one whole genome duplication occurred along the branch leading to <i>H. syriacus</i>.</span></p> <p class="BodyA"><span><b>Conclusions:</b> Here, we corroborated the independent genome doubling previously found in the lineage leading to <i>H. syriacus </i>and a shared genome doubling of this lineage and the remainder of <i>Hibiscus</i>. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within <i>Hibiscus</i>) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.</span></p>
Sequence alignments of Corallicolids, apicomplexan symbionts of coral
<p class="BodyA">Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called 'corallicolids', are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, <i>Gemmocystis cylindrus</i> (described from the coral <i>Dendrogyra cylindrus</i>), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single-cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, <i>Corallicola aquarius</i> gen. nov. sp. nov. from its <i>Rhodactis </i>sp.<i> </i>host, and also describe a second species, <i>Anthozoaphila gnarlus</i> gen. nov. sp. nov., from the coral host <i>Madracis mirabilis</i>. Finally, we propose reassigning the incertae sedis taxon <i>G. cylindrus</i> from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.</p>
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
Data from: Does thermal plasticity align with local adaptation? – An interspecific comparison of wing morphology in sepsid flies
Although genetic and plastic responses are sometimes considered as unrelated processes, their phenotypic effects may often align because genetic adaptation is expected to mirror phenotypic plasticity if adaptive, but run counter to it when maladaptive. The magnitude and direction of this alignment has further consequences for both the tempo and mode of adaptation. To better understand the interplay between phenotypic plasticity and genetic change in mediating adaptive phenotypic variation to climate variability, we here quantified genetic latitudinal variation and thermal plasticity in wing loading and wing shape in two closely related and widespread sepsid flies. Common garden rearing of 16 geographical populations reared across multiple temperatures revealed that wing loading decreases with latitude in both species. This pattern could be driven by selection for increased dispersal capacity in the cold. However, although allometry, sexual dimorphism, thermal plasticity and latitudinal differentiation in wing shape all show similar patterns in the two species, the relationship between the plastic and genetic response differed between them. While latitudinal differentiation (south to north) mirrored thermal plasticity (hot to cold) in Sepsis punctum, there was no relationship in Sepsis fulgens. While this suggests that thermal plasticity may have helped to mediate local adaptation in S. punctum, it also demonstrates that genetic wing shape differentiation and its relation to thermal plasticity may be complex and idiosyncratic, even among ecologically similar and closely related species. Hence, genetic responses can, but do not necessarily, align with phenotypic plasticity induced by changing environmental selection pressures.
Data from: Two influential primate classifications logically aligned
Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments—in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.
Data from: The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection
Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments.
Data from: Control of signaling alignment during the dynamic courtship display of a jumping spider
During communication, alignment between signals and sensors can be critical. Signals are often best perceived from specific angles, and sensory systems can also exhibit strong directional biases. However, we know little about how animals establish and maintain such signaling alignment during communication. To investigate this, we characterized the spatial dynamics of visual courtship signaling in the jumping spider Habronattus pyrrithrix. The male performs forward-facing displays involving complex color and movement patterns, with distinct long- and short-range phases. The female views displays with 2 distinct eye types and can only perceive colors and fine patterns of male displays when they are presented in her frontal field of view. Whether and how courtship interactions produce such alignment between male display and female field of view is unknown. We recorded relative positions and orientations of both actors throughout courtship and established the role of each sex in maintaining signaling alignment. Males always oriented their displays toward the female. However, when females were free to move, male displays were consistently aligned with female principal eyes only during short-range courtship. When female position was fixed, signaling alignment consistently occurred during both phases, suggesting that female movement reduces communication efficacy. When female models were experimentally rotated to face away during courtship, males rarely repositioned themselves to re-align their display. However, males were more likely to present certain display elements after females turned to face them. Thus, although signaling alignment is a function of both sexes, males appear to rely on female behavior for effective communication.
Peema perspective - Image alignment and Circular Dichroism calculation
<p>This movie describes how to use DAWN to process a set of PEEM data as acquired on the I06 beamline at Diamond Light Source</p>
Genome alignments from "Split-alignment of genomes finds orthologies more accurately"
<p>Here are the genome alignments resulting from "Split-alignment of genomes finds orthologies more accurately", Genome Biology 2015, 16:106.</p> <ul> <li>In the terminology of that paper, these are 2-split, post-masked alignments.</li> <li>They are in MAF format (http://genome.ucsc.edu/FAQ/FAQformat.html), with "p" lines (http://last.cbrc.jp/doc/last-split.html).</li> <li>Alignments with high ambiguity have not been removed, so if you want unambiguously 1-to-1 alignments, remove those annotated with mismap > 0.00001 or so.</li> <li>The chimp and orangutan alignments were made using the 500/30 gap costs suggested at the end of the paper.</li> </ul> <p> </p>
6255 gene alignments of Asellidae CDS
<p>Families of orthologous genes used in "<strong>No evidence that nitrogen limitation influences the elemental composition of isopod transcriptomes and proteomes"</strong></p> <p>The 6,255 alignments used in this publication are archived here. Each alignment corresponds to one "pattern" (~ gene family, except when one family X is composed of several patterns = e.g. multigenic family). Each alignment includes between 2 and 26 species. These alignments have been created with:</p> <ul> <li>prank -codon -F</li> <li>GBlocks -b5=h (to allow some gaps)</li> </ul> <p>Alignment are named according to the corresponding family_pattern, e.g. "FAM003424_1.fas.prank_codon.best.fas-gb.bis" corresponds to the family "003424" and the pattern "1". They are composed of several fasta sequences, each sequence corresponding to one species. The name of each fasta sequence starts with the species code (e: BMOV, PCANC) in upper letters. Gaps are present ("----"). ATTENTION: species order differs in each alignment!</p> <p> </p> <p>Table of the correspondance species - code:</p> <p>Species Code couple eco<br /> P. beticus PBTS c1 epi<br /> P. jaloniacus PJJ c1 hypo<br /> P. aragonensis PARE c2 epi<br /> P. spelaeus PSSE c2 hypo<br /> B. peltatus BPM c3 epi<br /> B. molinai BMOV c3 hypo<br /> P. ibericus PIBB c4 epi<br /> P. arthrodilus PATL c4 hypo<br /> P. meridianus PMLL c5 epi<br /> P. margalefi PMAF c5 hypo<br /> P. granandensis PGRP c6 epi<br /> P. solanasi PSOG c6 hypo<br /> P. coxalis PCOB c7 epi<br /> P. parvulus PPRS c7 hypo<br /> P. assaforensis PASA c8 epi<br /> P. rectus PRUE c8 hypo<br /> P. karamani PKK c9 epi<br /> P. hercegovinensis PHEZ c9 hypo<br /> P. coiffaiti PCOIP c10 epi<br /> P. cavaticus PCBF c10 hypo<br /> P. racovitzai PRBE c11 epi<br /> P. escolai PECD c11 hypo<br /> P. ortizi POJ c12 epi<br /> P. grafi PGC c12 hypo<br /> P. ebrensis PEF c13 epi<br /> P. cantabricus PCANC c13 hypo</p> <p>Remark: out of these 6,255 alignments, 8 alignments are empty (when Gblock has removed ALL aligned positions): [1] "FAM000157_5.fas" "FAM000587_3.fas" "FAM000615_1.fas" "FAM008836_1.fas" [5] "FAM013862_1.fas" "FAM015586_1.fas" "FAM017544_1.fas" "FAM022381_1.fas"</p> <p> </p>
Greengenes May 2013 unmasked 16S rRNA alignments
<p>These data are derived from the raw PyNast aligned 16S rRNA files from Greengenes. The Jupyter (Python 3) notebook used and the original data (provided by Greg Caporaso) are also included.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.