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Добірка наукової літератури з теми "Synteny analysis"

Автор: Grafiati

Опубліковано: 2 лютого 2024

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Статті в журналах з теми "Synteny analysis"

Han, F., A. Kleinhofs, S. E. Ullrich, A. Kilian, M. Yano, and T. Sasaki. "Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions." Genome 41, no. 3 (June 1, 1998): 373–80. http://dx.doi.org/10.1139/g98-027.

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Анотація:

The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.

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Pandey, Manmohan, Basdeo Kushwaha, Ravindra Kumar, Prachi Srivastava, Suman Saroj, and Mahender Singh. "Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes." Journal of Heredity 111, no. 5 (July 2020): 486–90. http://dx.doi.org/10.1093/jhered/esaa025.

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Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

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Lee, Jongin, Woon-young Hong, Minah Cho, Mikang Sim, Daehwan Lee, Younhee Ko, and Jaebum Kim. "Synteny Portal: a web-based application portal for synteny block analysis." Nucleic Acids Research 44, W1 (May 6, 2016): W35—W40. http://dx.doi.org/10.1093/nar/gkw310.

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Morán Losada, Patricia, and Burkhard Tümmler. "SNP synteny analysis ofStaphylococcus aureusandPseudomonas aeruginosapopulation genomics." FEMS Microbiology Letters 363, no. 19 (October 2016): fnw229. http://dx.doi.org/10.1093/femsle/fnw229.

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Zhao, Tao, and M. Eric Schranz. "Network approaches for plant phylogenomic synteny analysis." Current Opinion in Plant Biology 36 (April 2017): 129–34. http://dx.doi.org/10.1016/j.pbi.2017.03.001.

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Pan, X., L. Stein, and V. Brendel. "SynBrowse: a synteny browser for comparative sequence analysis." Bioinformatics 21, no. 17 (June 30, 2005): 3461–68. http://dx.doi.org/10.1093/bioinformatics/bti555.

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Xu, Yiqing, Changwei Bi, Guoxin Wu, Suyun Wei, Xiaogang Dai, Tongming Yin, and Ning Ye. "VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/7823429.

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Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF). Result. Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.

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Stirling, Brigid, Zamin Koo Yang, Lee E. Gunter, Gerald A. Tuskan, and H. D. Bradshaw Jr. "Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity." Canadian Journal of Forest Research 33, no. 11 (November 1, 2003): 2245–51. http://dx.doi.org/10.1139/x03-155.

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More than 300 kb of DNA sequence from five Populus bacterial artificial chromosome (BAC) clones was compared with the complete sequence of the Arabidopsis genome to search for collinearity between the genomes of these two plant genera. Approximately 27% of the DNA sequences from the Populus genome were homologous to protein-coding regions in the Arabidopsis genome. BLAST scores and synteny were used to infer orthologous relationships between the Populus and Arabidopsis homologs. The probability that any pair of genes on a single Populus BAC will have orthologs on the same Arabidopsis chromosome is 46%58%, substantially greater than the 20% expectation if there is no conservation of synteny between the Populus and Arabidopsis genomes. Likewise, the probability that any pair of genes on a single Populus BAC will have orthologs on a single Arabidopsis BAC is 19%25%, much higher than the 0.1% expected if the orthologs are randomly distributed. These results provide evidence for substantial "pockets" of conserved microcollinearity between regions of the Populus and Arabidopsis genomes as well as for conservation of synteny even when local gene collinearity is not preserved during genome evolution.

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Kato, K., H. Miura, and S. Sawada. "Comparative mapping of the wheat Vrn-AI region with the rice Hd-6 region." Genome 42, no. 2 (April 1, 1999): 204–9. http://dx.doi.org/10.1139/g98-115.

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Although extensive synteny between hexaploid wheat and rice chromosomes has been demonstrated, synteny between the species breaks down in several regions of the wheat genome carrying agronomically important genes. A possible relationship between the wheat Vrn-A1, the vernalization response gene on chromosome 5A, and the rice Hd-6, a QTL controlling heading date by photoperiod response on chromosome 3, was investigated. Rice cDNA clones which had previously been mapped onto the Hd-6 region were screened for comparative genetic mapping of the Vrn-A1 region. Ten markers mapped to Hd-6 were assigned to wheat chromosome 5A by nullisomic-tetrasomic analysis. Of them, four cDNA markers, linked within 2.2 cM in the rice Hd-6 region, were mapped on the flanking region of the wheat Vrn-A1, with a complete correspondence of order, demonstrating a fine-scale genetic collinearity. These results gave evidence that the wheat Vrn-A1 region is in synteny with the rice Hd-6 region.Key words: wheat, rice, vernalization response gene, photoperiod response gene, synteny.

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Matsunaga, Sachihiro, and Akihiro Nakaya. "Computational Synteny Analysis Promotes a Better Understanding of Chromosome Evolution." CYTOLOGIA 82, no. 2 (2017): 101–4. http://dx.doi.org/10.1508/cytologia.82.101.

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Більше джерел

Дисертації з теми "Synteny analysis"

Restrepo, Montoya Daniel. "Computational Identification, Phylogenetic and Synteny Analysis of Receptor-Like Kinases “RLK” and Receptor-Like Proteins “RLP” in Legumes." Diss., North Dakota State University, 2018. https://hdl.handle.net/10365/29870.

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Legumes are considered the second most important family of crop plants after the grass family based on economic relevance. In recent years, the field of legume genomics has expanded due to advancements in high-throughput sequencing and genotyping technologies. To date, no published comparative genomic analysis explores receptor-like kinases “RLK” and receptor-like proteins “RLP” among legume genomes. Evaluating these RLK and RLP should provide a source of new information because extensive genetic and phenotypic studies have already discovered the diverse roles of RLK and RLP in cell development, disease resistance, and stress responses among other functions. This study demonstrates that a computational logical approach for classifying the RLK/RLP in legumes/non-legumes is statistically well supported and can be used in other plant species. The analysis of RLK/RLP of 7 legumes and 3 non-legume species evaluated suggests that about 2% are RLK and less than 1% of the proteins are RLP. The results suggest a dynamic evolution of RLK and RLP in the legume family. In fact, between 66% to 85% of RLK and 83% to 88% of RLP belong to orthologous clusters among the species evaluated. The remaining RLK and RLP proteins are classified as singletons. The ratio of the pairwise synteny blocks of RLK/RLP among legumes shows a 1:1 relationship. The exception is G. max, which shows an approximately 2:1 ratio due to its recent whole genome duplication (G. max vs. the other six legumes). The other legumes show evidence of a similar proportion of plasma membrane proteins among the legume pairwise synteny blocks.
Fulbright Scholarship
Francisco Jose de Caldas (Colciencias, Colombia) Scholarship
North Dakota State University. Dry Breeding Program

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Wasikowski, Rachael A. "The Maize TFome 2.0: Genomic Analysis of Transcription Factor Repertoire." University of Toledo / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=toledo152545363525107.

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Olinski, Robert Piotr. "Evolutionary Analysis of the Insulin-Relaxin Gene Family from the Perspective of Gene and Genome Duplication Events." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7892.

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Lariviere, Delphine. "Méthodes bioinformatiques d'analyse de l'histoire évolutive des familles de gènes ˸ intégration de données, indices évolutifs, et analyses fonctionnelles appliquées aux familles de gènes impliquées dans la réponse des plantes aux stress environnementaux." Electronic Thesis or Diss., Montpellier, SupAgro, 2016. http://www.theses.fr/2016NSAM0041.

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L'étude des familles de gènes et de leur histoire évolutive apporte des indices précieux pour l'annotation fonctionnelle. En effet, le transfert d’annotations fonctionnelles entre gènes dépend de leur histoire évolutive, que cela soit l’histoire des duplications ou la simple divergence de séquence. Afin d'aider la compréhension des familles de gènes, la reconstruction de l'histoire évolutive doit être associée à des annotations et indices fonctionnels liés aux gènes de la famille. Cette reconstruction de l'histoire évolutive des familles passe par l'intégration de plusieurs données hétérogènes. Les indices évolutifs peuvent provenir de plusieurs sources et faire appel à différents outils, il est alors important de bien identifier quelles sont les informations nécessaires à ces études, mais aussi de rendre possible leur intégration dans une analyse commune adapté aux organismes étudiés. Après avoir étudié les spécificités des génomes de plantes et les modes d'évolution spécifiques des familles de gènes nous avons apporté une réponse à cette problématique en développant un système intégratif dédié à l'analyse des familles de gènes, et particulièrement des familles de gènes impliquées dans la réponse aux stress environnementaux. Ce système contient un ensemble d'outils sélectionnés incluant une méthode originale d'intégration des données de synténie, et propose une visualisation synthétique des informations nécessaire à l'étude des familles de gènes. Ce système a été appliqué à l'analyse de familles d'intérêt impliquées dans la résistance aux stress abiotiques, qui nous permet de discuter de l'apport de ce système à l'étude des familles de gènes
The study of gene families and their evolutive history brings precious evidences for the functional annotation of families. The functional transfer depends on one hand on the relationship between genes, and on another hand on the sequence divergence. In order to facilitate the comprehension of gene families, the inference of their evolutive history must be correlated to functional evidences and annotations. This inference is possible through the integration of several heterogeneous data. Evolutive evidences can come from several different data sources and need several tools . It is therefore important to clearly identify both these sources and tools, but also to implement their integration in a common analysis specific to the studied organisms. After studying plant genomes specificities, and their specific mode of evolution, we responded to this problematic through the development of an integrative system containing expertingly chosen data, and implemented tools dedicated to the analysis of gene families. The system also propose a synthetic visualisation analytic tool and an original method to integrate syntenic data for gene family analysis. This system has then been used to study gene family of interest, implied in abiotic stress resistance in plants, that allows us to discuss the intake of the system for gene family analysis

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Nordahl, Åke. "Metoder för informationsoptimering vid organisk syntes." Doctoral thesis, Umeå universitet, Kemiska institutionen, 1990. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-102557.

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Bederr, Nassima. "Comparative analyses of regions of the puffer fish (Fuga rubripes) genome sharing synteny with human chromosome 9q34." Thesis, Open University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288360.

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Zhou, Xiamo. "OSTE Microfluidic Technologies for Cell Encapsulation and Biomolecular Analysis." Doctoral thesis, KTH, Mikro- och nanosystemteknik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-217995.

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In novel drug delivery system, the encapsulation of therapeutic cells in microparticles has great promises for the treatment of a range of health con- ditions. Therefore, the encapsulation material and technology are of great importance to the validity and efficiency of the advanced medical therapy. Several unsolved challenges in regards to versatile microparticle synthesis ma- terials and methods form the main obstacle for a translation of novel cell therapy concepts from research to clinical practice. Thiol-ene based polymer systems have emerged and gained great popular- ity in material development in general and in biomedical applications specif- ically. The thiol-ene platform is broad and therefore of interest for a variety of applications. At the same time, many aspects of this material platform are largely unexplored, for example material and manufacturing technology developments for microfluidic applications . In this Ph.D. thesis, thiol-ene materials are explored for use in cell encap- sulation. The marriage of these two technology fields breeds the possibility for a novel microfluidic cell encapsulation approach using a novel encapsulation material. To this end, several new manufacturing technologies for thiol-ene and thiol-ene-epoxy droplet microfluidic devices were developed. Moreover, core-shell microparticle synthesis for cell encapsulation based on a novel co- synthesis concept using a thiol-ene based material was developed and inves- tigated. Finally, a thiol-ene-epoxy system was also used for the formation of microwells and microchannels that improve protein analysis on microarrays. The first part of the thesis presents the background and state-of-the-art technologies in regards to cell therapy, microfluidics, and thiol-ene based ma- terials. In the second part of the thesis, a novel manufacturing approach of thiol-ene-epoxy material as well as core-shell particle co-synthesis in micro- fluidics using thiol-ene based material are presented and characterized. The third part of the thesis presents the cell viability studies of encapsulated cells using the novel encapsulation material and method. In the final part of the thesis, two applications of thiol-ene-epoxy gaskets for protein detection mi- croarrays are presented.
Inkapsling av levande celler i mikrokapslar för terapeutiska ändamål är mycket lovande för frmatida behandling av många olika sjukdomar. Emeller- tid är en behandlings effektivitet i hög grad beroende av vilka material som används för inkapsling och vilken teknisk lösning som används för att ska- pa mikrokapslarna. För närvarande återstår det många utmaningar för att omvandla grundforskningresultat till klinisk verklighet, vilken kräver mer än- damålsenliga tillvägagångssätt för att tillverka mikrokapslar i material som är kompatibla med användningsområdena. De senaste åren har tiol-en baserade polymerer har blivit mycket använda för materialutveckling i stort och för biomedicinska tillämpningar i synnerhet. Med tiol-en kemi kan en mycket stor mängd helt olika syntetiska material framställas, vilket gör tiol-ener intressanta för en mängd applikationer. För närvarande är dock mycket inom denna materialklass outforskat, t.ex. inom material och tillverkningmetodik för mikrofluidiktillämpningar. I denna avhandling används tiol-ener för cellinkapsling. Sammanslagning av dessa teknologier möjliggör en ny typ av cellinkapsling med nya materi- alegenskaper. En mängd olika tillverkningssätt där tiol-en eller tiol-en-epoxi används för droplet-mikrofluidiksystem utvecklades. Core-shell mikrokapsel- syntes för cell-inkapsling baserat på en ny metod för samtidig syntes av både core och shell utvecklades och karaktäriserades. Slutligen utvecklades ett tiol- en-epoxi system för enkel integrering med proteinmikroarrayer på objektsglas. I avhandlingens första del presenteras bakgrund och dagens bästa teknolo- gier för terapeutisk cellinkapsling, mikrofluidik och tiol-en baserade material. I avhandlingens andra del presenteras en ny tillverkningsmetod för mikro- strukturerade tiol-en-epoxi artiklar och samtidig syntes av core och shell för mikrokapslar med användande av mikrofluidik. I den tredje delen presenteras cellöverlevandsstudier för de celler som inkapslats med de nya materialen och de nyutvecklade metoderna. I den avslutande delen beskrivs två specifika fall där tiol-en-epoxi komponenter används för proteindetektion och mikroarrayer.

QC 20171122

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Poirion, Olivier. "Discrimination analytique des génomes bactériens." Thesis, Ecully, Ecole centrale de Lyon, 2014. http://www.theses.fr/2014ECDL0033/document.

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Le génome bactérien est classiquement pensé comme constitué de “chromosomes”, éléments génomiques essentiels pour l’organisme, stables et à évolution lente, et de “plasmides”, éléments génomiques accessoires, mobiles et à évolution rapide. La distinction entre plasmides et chromosomes a récemment été mise en défaut avec la découverte dans certaines lignées bactériennes d’éléments génomiques intermédiaires, possédant à la fois des caractéristiques de chromosomes et de plasmides. Désignés par le terme de “chromosomes secondaires”, “mégaplasmides” ou “chromid”, ces éléments sont dispersés parmi les lignées bactériennes et sont couramment décrits comme des plasmides adaptés et modifiés. Cependant, leur véritable nature et les mécanismes permettant leur intégration dans le génome stable reste à caractériser. En utilisant les protéines liées aux Systèmes de Transmission de l’Information Génétique (STIG) comme variables descriptives des éléments génomiques bactériens (ou réplicons), une étude globale de génomique comparative a été conduite sur l’ensemble des génomes bactériens disponibles. A travers l’analyse de l’information contenue dans ce jeu de données par différentes approches analytiques, il apparait que les STIG constituent des marqueurs pertinents de l’état d’intégration des réplicons dans le génome stable, ainsi que de leur origine évolutive, et que les Réplicons Extra-Chromosomiques Essentiels (RECE) témoignent de la diversité des mécanismes génétiques et des processus évolutifs permettant l’intégration de réplicons dans le génome stable, attestant ainsi de la continuité du matériel génomique
The genome of bacteria is classically separated into essential, stable and slow evolving replicons (chromosomes) and accessory, mobile and rapidly evolving replicons (plasmids). This paradigm is being questioned since the discovery of extra-chromosomal essential replicons (ECERs), be they called ”megaplasmids”, ”secondary chromosomes” or ”chromids”, which possess both chromosomal and plasmidic features. These ECERs are found in diverse lineages across the bacterial phylogeny and are generally believed to be modified plasmids. However, their true nature and the mechanisms permitting their integration within the sable genome are yet to be formally determined. The relationships between replicons, with reference to their genetic information inheritance systems (GIIS), were explored under the assumption that the inheritance of ECERs is integrated to the cell cycle and highly constrained in contrast to that of standard plasmids. A global comparative genomics analysis including all available of complete bacterial genome sequences, was performed using GIIS functional homologues as parameters and applying several analytical procedures. GIIS proved appropriate in characterizing the level of integration within the stable genome, as well as the origins, of the replicons. The study of ECERs thus provides clues to the genetic mechanisms and evolutionary processes involved in the replicon stabilization into the essential genome and the continuity of the genomic material

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Asbayou, Omar. "L'identification des entités nommées en arabe en vue de leur extraction et classification automatiques : la construction d’un système à base de règles syntactico-sémantique." Thesis, Lyon, 2016. http://www.theses.fr/2016LYSE2136.

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Cette thèse explique et présente notre démarche de la réalisation d’un système à base de règles de reconnaissance et de classification automatique des EN en arabe. C’est un travail qui implique deux disciplines : la linguistique et l’informatique. L’outil informatique et les règles la linguistiques s’accouplent pour donner naissance à une nouvelle discipline ; celle de « traitement automatique des langues », qui opère sur des niveaux différents (morphosyntaxique, syntaxique, sémantique, syntactico-sémantique etc.). Nous avons donc, dans ce qui nous concerne, mis en œuvre des informations et règles linguistiques nécessaires au service du logiciel informatique, qui doit être en mesure de les appliquer, pour extraire et classifier, par des annotations syntaxiques et/ou sémantiques, les différentes classes d’entités nommées.Ce travail de thèse s’inscrit donc dans un cadre général de traitement automatique des langues, mais plus particulièrement dans la continuité des travaux réalisés au niveau de l’analyse morphosyntaxique par la conception et la réalisation des bases des données lexicales SAMIA et ensuite DIINAR avec l’ensemble de résultats de recherches qui en découlent. C’est une tâche qui vise à l’enrichissement lexical par des entités nommées simples et complexes, et qui veut établir la transition de l’analyse morphosyntaxique vers l’analyse syntaxique, et syntatico-sémantique dans une visée plus générale de l’analyse du contenu textuel. Pour comprendre de quoi il s’agit, il nous était important de commencer par la définition de l’entité nommée. Et pour mener à bien notre démarche, nous avons distingué entre deux types principaux : pur nom propre et EN descriptive. Nous avons aussi établi une classification référentielle en se basant sur diverses classes et sous-classes qui constituent la référence de nos annotations sémantiques. Cependant, nous avons dû faire face à deux difficultés majeures : l’ambiguïté lexicale et les frontières des entités nommées complexes. Notre système adopte une approche à base de règles syntactico-sémantiques. Il est constitué, après le Niveau 0 d’analyse morphosyntaxique, de cinq niveaux de construction de patrons syntaxiques et syntactico-sémantiques basés sur les informations linguistique nécessaires (morphosyntaxiques, syntaxiques, sémantique, et syntactico-sémantique). Ce travail, après évaluation en utilisant deux corpus, a abouti à de très bons résultats en précision, en rappel et en F–mesure. Les résultats de notre système ont un apport intéressant dans différents application du traitement automatique des langues notamment les deux tâches de recherche et d’extraction d’informations. En effet, on les a concrètement exploités dans les deux applications (recherche et extraction d’informations). En plus de cette expérience unique, nous envisageons par la suite étendre notre système à l’extraction et la classification des phrases dans lesquelles, les entités classifiées, principalement les entités nommées et les verbes, jouent respectivement le rôle d’arguments et de prédicats. Un deuxième objectif consiste à l’enrichissement des différents types de ressources lexicales à l’instar des ontologies
This thesis explains and presents our approach of rule-based system of arabic named entity recognition and classification. This work involves two disciplines : linguistics and computer science. Computer tools and linguistic rules are merged to give birth to a new discipline : Natural Languge Processsing, which operates in different levels (morphosyntactic, syntactic, semantic, syntactico-semantic…). So, in our particular case, we have put the necessary linguistic information and rules to software sevice. This later should be able to apply and implement them in order to recognise and classify, by syntactic and semantic annotations, the different named entity classes.This work of thesis is incorporated within the general domain of natural language processing, but it particularly falls within the scope of the continuity of the accomplished work in terms of morphosyntactic analysis and the realisation of lexical data bases of SAMIA and then DIINAR as well as the accompanying scientific recearch. This task aimes at lexical enrichement with simple and complex named entities and at establishing the transition from the morphological analysis into syntactic and syntactico-semantic analysis. The ultimate objective is text analysis. To understand what it is about, it was important to start with named entity definition. To carry out this task, we distinguished between two main named entity types : pur proper name and descriptive named entities. We have also established a referential classification on the basis of different classes and sub-classes which constitue the reference for our semantic annotations. Nevertheless, we are confronted with two major difficulties : lexical ambiguity and the frontiers of complex named entities. Our system adoptes a syntactico-semantic rule-based approach. After Level 0 of morpho-syntactic analysis, the system is made up of five levels of syntactic and syntactico-semantic patterns based on tne necessary linguisic information (i.e. morphosyntactic, syntactic, semantic and syntactico-semantic information).This work has obtained very good results in termes of precision, recall and F-measure. The output of our system has an interesting contribution in different applications of the natural language processing especially in both tasks of information retrieval and information extraction. In fact, we have concretely exploited our system output in both applications (information retrieval and information extraction). In addition to this unique experience, we envisage in the future work to extend our system into the sentence extraction and classification, in which classified entities, mainly named entities and verbs, play respectively the role of arguments and predicates. The second objective consists in the enrichment of different types of lexical resources such as ontologies

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Naňo, Andrej. "Automatické generování testovacích dat informačních systémů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2021. http://www.nusl.cz/ntk/nusl-445520.

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ISAGENis a tool for the automatic generation of structurally complex test inputs that imitate real communication in the context of modern information systems . Complex, typically tree-structured data currently represents the standard means of transmitting information between nodes in distributed information systems. Automatic generator ISAGENis founded on the methodology of data-driven testing and uses concrete data from the production environment as the primary characteristic and specification that guides the generation of new similar data for test cases satisfying given combinatorial adequacy criteria. The main contribution of this thesis is a comprehensive proposal of automated data generation techniques together with an implementation, which demonstrates their usage. The created solution enables testers to create more relevant testing data, representing production-like communication in information systems.

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Книги з теми "Synteny analysis"

Dobrzyńska, Teresa. Tekst: Próba syntezy. Warszawa: Instytut Badań Literackich, 1993.

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Witkowski, Stanisław. Synteza i badania strukturalne pochodnych witaminy E: Rozprawa habilitacyjna. Białystok: Instytut Chemii, 2004.

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Trzaska, Zdzisław. Analiza, identyfikacja i synteza obwodów dynamicznych metodą zmiennych stanu drugiego rzędu. Warszawa: Wydawn. Politechniki Warszawskiej, 1987.

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Synteza I Badania Strukturalne Pochodnych Witaminy E: Rozprawa Habilitacyjna. Instytut Chemii, 2004.

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Ltd, ICON Group, and ICON Group International Inc. SYNTEL, INC.: Labor Productivity Benchmarks and International Gap Analysis (Labor Productivity Series). 2nd ed. Icon Group International, 2000.

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Ltd, ICON Group. SYNTEL, INC.: International Competitive Benchmarks and Financial Gap Analysis (Financial Performance Series). 2nd ed. Icon Group International, 2000.

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Ltd, ICON Group, and ICON Group International Inc. SIAM SYNTECH CONSTRUCTION PUBLIC CO LTD: International Competitive Benchmarks and Financial Gap Analysis (Financial Performance Series). 2nd ed. Icon Group International, 2000.

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Частини книг з теми "Synteny analysis"

Doerr, Daniel, and Bernard M. E. Moret. "Sequence-Based Synteny Analysis of Multiple Large Genomes." In Comparative Genomics, 317–29. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_11.

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Miao, Hongmei, Yamin Sun, Wenchao Lin, Lei Wang, and Haiyang Zhang. "Genome Synteny Analysis and Phylogenetic Position of S. indicum." In Compendium of Plant Genomes, 267–73. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-319-98098-0_16.

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Kuravadi, Nagesh A., and Malali Gowda. "Comparison of Gene Families and Synteny Analysis from Neem Genome." In The Neem Genome, 93–97. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-16122-4_10.

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James, Timothy Y. "Analysis of Mating-Type Locus Organization and Synteny in Mushroom Fungi: Beyond Model Species." In Sex in Fungi, 317–31. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815837.ch19.

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Sen, Gao, Yuan Zihao, Ning Li, Jiaren Zhang, and Zhanjiang Liu. "Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses." In Bioinformatics in Aquaculture, 30–42. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781118782392.ch2.

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Craig, Jeff. "Isolation of vertebrate metaphase chromosomes and their analysis by FISH." In Chromosome Structural Analysis, 59–80. Oxford University PressOxford, 1992. http://dx.doi.org/10.1093/oso/9780199636990.003.0004.

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Abstract This chapter concentrates on the in situ hybridization of DNA probes to metaphase chromosomes isolated from vertebrate cells. Fluorescence in situ hybridization (FISH) has a number of applications within the field of chromosome structure, ranging from the simple mapping of specific genes or markers (1-3), mapping transgene integration sites (4-7), through to analysis of the distribution of particular classes of DNA sequence across the genome, e.g. repeat sequence families (6--10), CpG islands (11), fractions of defined base composition (12), and scaffold or matrix-associated sites (13). Whole chromosomes can also be highlighted by chromosome painting probes (14, 15, and Chapter 6), and interspecies hybridization can highlight regions of conserved synteny (16, 17). There are also other novel applications of FISH in studies of chromosome structure, these either analyse karyotype changes or explore the higher order organization of chromosomes (18-24).

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Momand, Jamil, Alison Mccurdy, Silvia Heubach, and Nancy Warter-Perez. "Genomics." In Concepts in Bioinformatics and Genomics. Oxford University Press, 2017. http://dx.doi.org/10.1093/hesc/9780190610548.003.0009.

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This chapter displays genomics analysis with an emphasis on next-generation sequencing (NGS), and annotation of bacterial genomes. It uncovers the underlying principles of dideoxy sequencing and selected next-generation sequencing technologies. The chapter also examines the theory of polymerase chain reaction (PCR) and the general categories of DNA that constitute the human genome (the genomic landscape). The chapter then shifts to investigate how DNA fingerprinting is performed and the degree of synteny shared between genomes. It reviews the whole genome shotgun strategy approach to genome sequencing, then examines how gene prediction software programs predict and annotate genes in genomes. Finally, the chapter describes the haplotype, the HapMap Project, and the significance of the HapMap project. It then looks into the benefits and concerns of having knowledge of personal genome data.

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Niszczota, Paweł. "Grzeszne spółki: synteza 15 lat badań teoretycznych i empirycznych." In Ekonomia i inne nauki społeczne. Studia interdyscyplinarne, 133–50. Wydawnictwo Uniwersytetu Ekonomicznego w Poznaniu, 2023. http://dx.doi.org/10.18559/978-83-8211-192-7/8.

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Sin stocks: A synthesis of 15 years of theoretical and empirical studies. In the narrowest sense, sin stocks are shares in companies engaged in the production of alcohol, tobacco, or gambling. Starting with the article by Hong and Kacperczyk (2009), they have been attracting an increasing interest from researchers. In this article, I attempt to synthesize recent theoretical and empirical work on morally controversial companies, by presenting (1) differences in the way sin stocks are defined, (2) work on estimating the sin stock premium, (3) determinants of propensity to invest in sin stocks, and (4) studies analysing selected cases in which sinful investments can be perceived differently. These could include (a) delegating investment decisions to fund managers who have behaved nobly in the past, (b) delegating decisions to algorithms, and (c) short-selling sin stocks. Additionally, I present several potential directions for researchers interested in sin stocks.

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Bacolod, Manny D., Swadesh K. Das, Upneet K. Sokhi, Steven Bradley, David A. Fenstermacher, Maurizio Pellecchia, Luni Emdad, Devanand Sarkar, and Paul B. Fisher. "Examination of Epigenetic and other Molecular Factors Associated with mda-9/Syntenin Dysregulation in Cancer Through Integrated Analyses of Public Genomic Datasets." In Advances in Cancer Research, 49–121. Elsevier, 2015. http://dx.doi.org/10.1016/bs.acr.2015.04.006.

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Тези доповідей конференцій з теми "Synteny analysis"

Потокина, Е. К., Е. А. Григорьева, В. А. Волков та П. С. Ульянич. "COMPARISON OF GENOME ASSEMBLIES AND SYNTENY ANALYSIS OF VVITIS VINIFERA L. И VITIS ROTUNDIFOLIA Michaux." У Материалы I Всероссийской научно-практической конференции с международным участием «Геномика и современные биотехнологии в размножении, селекции и сохранении растений». Crossref, 2020. http://dx.doi.org/10.47882/genbio.2020.53.18.022.

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Zaccaron, Alex. "Impact of genomic structural variations on virulence of the tomato pathogen Cladosporium fulvum." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-1.

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Cladosporium fulvum causes tomato leaf mold and has been extensively used in the past as a model species to study plant-microbe interactions. Although the first chromosome-scale reference genome of the fungus was released in 2022, still little is known about how its genome architecture and structural variations (SVs) thereof impact its virulence. In this study, we used PacBio HiFi to sequence the genomes of four additional C. fulvum isolates and further assembled them at chromosome level. Comparative genome analyses revealed high chromosomal synteny among the five isolates, and a set of 13 core and two dispensable chromosomes, one of which carries pseudogenized copies of effector genes and likely emerged by duplication of subtelomeric regions of core chromosome. Between 14906 and 14993 genes were predicted in each C. fulvum genome with an estimated completeness of >99%. A pangenome analysis of the five isolates revealed a low number of 331 accessory genes, indicating high conservation of gene content among isolates of the fungus. An analysis of SVs showed no enriched of effectors or of other pathogenicity-related genes in these regions. However, SVs in subtelomeric regions affected virulence by prompting the loss of effector genes residing in them, as we have found is the case for the Avr9 effector gene of C. fulvum. Collectively, these results provide new insights of how genomic SVs can contribute to virulence of fungal pathogens.

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Datsko, Bohdan. "Syntesys of Anti-Corrosion Pigment Based on Nanoporous Zeolite and Zinc Monophosphate." In International Young Scientists Conference on Materials Science and Surface Engineering. Karpenko Physico-Mechanical Institute of the NAS of Ukraine, 2023. http://dx.doi.org/10.15407/msse2023.167.

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Ecologically safe pigments based on synthetic zeolite and monophosphates of zinc, calcium and manganese were obtained by mechanochemical synthesis. The optimal conditions for their dispersion were established: 200 rpm for 60 min. Using the method of electron microscopy and energy dispersive analysis, the surface morphology and elemental composition of the obtained pigment were determined, which indicates the intercalation of phosphorus and relevant metals into the zeolite structure.

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Звіти організацій з теми "Synteny analysis"

Grumet, R., J. Burger, Y. Tadmor, A. Gur, C. Barry, A. Schäffer, and M. Petreikov. Cucumis fruit surface biology: Genetic analysis of fruit exocarp features in melon (C. melo) and cucumber (C. sativus). Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134155.bard.

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The fruit surface (exocarp) is a unique tissue with multiple roles influencing fruit growth and development, disease susceptibility, crop yield, post-harvest treatments, shipping and storage quality, and food safety. Furthermore, highly visible exocarp traits are the consumer's first exposure to the fruit, serving to identify fruit type, variety, attractiveness, and market value. Cucurbit fruit, including the closely related Cucumis species, melon (C. melo) and cucumber (C. sativus), exhibit tremendous diversity for fruit surface properties that are not present in model species. In this project, we identified genetic factors influencing Cucumis fruit surface morphology with respect to important quality determinants such as exocarp and flesh color, cuticle deposition, and surface netting. We employed a combination of approaches including: genome-wide association studies (GWAS) utilizing an extensive melon population and the U.S. Plant Introduction (PI) collection for cucumber to identify genomic regions associated with natural variation in fruit surface traits; bulked segregant RNA-seq (BSR-seq) analysis of bi-parental F2:3 or RIL (recombinant inbred line) populations to genomic regions and candidate genes segregating for fruit surface traits; and comparison of syntenic genomic regions and identification of homologous candidate genes. Candidate genes were examined for sequence and/or expression differences during fruit development that correspond with phenotypic differences. Primary outcomes of the work included identification of candidate genes influencing cuticle deposition, epidermal cell structure, surface netting, and intensity of rind and flesh color. Parallel studies identified mutations within the cucumber and melon homologs of the transcription factor WIN1 (WAX INDUCER1) as a significant factor influencing these surface properties. Additional QTL (quantitative trait loci) were identified in both species, and candidate genes in melon include a novel beta-glucosidase involved in lignin production and an integral membrane protein potentially involved in cuticle metabolism. Genetic resources and biochemical approaches have been developed to study cuticle and wax deposition in both species: segregating populations of melon were developed and sequenced for bulked segregant analysis and samples collected for metabolic analysis; an isolation procedure was developed for lipid droplets from cucumber peel and metabolomic analyses have been initiated. Genetic studies in melon identified mutations in a candidate gene (APRR2), associated with light immature rind, and further indicated that this gene is also associated with color intensity of both mature rinds and flesh, making it a good target for breeding. GWAS studies utilizing the cucumber core diversity population are being performed to identify additional sources of variation for fruit surface properties, map QTL, and examine for synteny with melon. Collectively these studies identified genetic regions associated with important quality traits and contributed to our understanding of underlying biological processes associated with fruit surface development. Knowledge of genetic control of these characteristics can facilitate more efficient breeding for important fruit surface traits.

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Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.

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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.

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