Ortholog metrics are calculated for some groups of species, and these are used to classify a "high confidence" set of orthologs. The methodology uses two orthogonal sources of information, gene order conservation (GOC) and whole genome alignments (WGA).. The "GOC score" metric for a pair of orthologs measures whether the two genes up- and downstream of each gene in the ortholog pair are also orthologous, and allows for inversions and gene insertions. The "WGA coverage" metric determines the extent to which the orthologous regions have been aligned by pairwise LASTz alignments, primarily based on exonic coverage, with a small contribution from intronic coverage. Both metrics have a value between 0 and 100.. There is only an expectation for gene order conservation between species that are evolutionarily close; thus the GOC score is only calculated within Diptera, Chelicerata, and Hemiptera. Similarly, pairwise WGAs, and thus the related metric, are only available for a subset of fairly ...
The genome of an organism can be represented as a sequence of signed numbers. A natural question to investigate is how related two genomes are based on certain biologically plausible operations on their sequences. The canonical operation that has been considered is the inversion (or reversal) and the relative similarity between two genomes has been measured by finding the minimum numberof inversions that turn one sequence into another. Ten years ago Hannenhalli and Pevzner developed a rich theory and founda polynomial time algorithm to compute this distance for any two sequences, each with exactly one copy of a given number. Since then the theory has been refined and extended (to handle insertion/deletions) but there has existed no method to deal with two arbitrary sequences. In this presentation we investigate what operations are needed in orderto find a plausible distance between arbitrary sequences and show the techniques we are developing to handle them ...
Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing avail- ability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: Small Parsimony Problem (SPP) and Big Parsimony Problem (BPP). Maximum parsimony is a popular approach for SPP and BPP which relies on itera- tively solving a NP-hard problem, the median problem. As a result, current median solvers and phylogenetic inference methods based on the median problem all face se- rious problems on scalability and cannot be applied to datasets with large and distant genomes. In this thesis, we propose a new median solver for gene order data that combines double-cut-join (DCJ) sorting with the Simulated Annealing algorithm (SA- Median). Based on this median solver, we built a new phylogenetic inference method to solve both SPP and BPP problems
UNLABELLED GeneSyn is a software tool that allows automatic detection of conserved gene order from annotated genomes. AVAILABILITY Available free of charge for Unix/Linux/Cygwin platforms at ftp://159.149.110.11/pub/GeneSyn_1.0/ SUPPLEMENTARY INFORMATION ftp://159.149.110.11/pub/GeneSyn_1.0/
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The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3 gene is Hox5. (The gene order is : 5-Hox1,2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5 - 3). The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.
(2000) Wilson et al. Molecular Biology and Evolution. The complete sequence of the mitochondrial genome of the giant tiger prawn, Penaeus monodon (Arthropoda, Crustacea, Malacostraca), is presented. The gene content and gene order are identical to tho...
NORM-atlas gir tilgang til databasen i NORM for utvalgte bakteriearter og antibiotika over tid og fordelt på regioner. Verktøyet fremstiller norske resistensdata for ulike kliniske prøvematerialer, enten som andel resistente mikrober (R) eller samlet andel mikrober med resistens og intermediær følsomhet (R + I). Resistente mikrober (R) kan ikke behandles med det aktuelle antibiotikum. Mikrober som er intermediært følsomme (I) er forandret i forhold til villtypen, men kan fortsatt behandles dersom man bruker en høyere dose eller det aktuelle antibiotikum har en høy konsentrasjon på infeksjonsstedet. Andel med resistens og intermediær følsomhet (R + I) uttrykker samlet resistensutvikling ...
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Nowadays we are in the big data era. The high-dimensionality ofdata imposes big challenge on how to process them effectively andefficiently. Fortunately, in practice data are not unstructured.Their samples usually lie around low-dimensional manifolds andhave high correlation among them. Such characteristics can beeffectively depicted by low rankness. As an extension to thesparsity of first order data, such as voices, low rankness is alsoan effective measure for the sparsity of second order data, suchas images. In this paper, I review the representative theories,algorithms and applications of the low rank subspace recoverymodels in data processing.
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Geneticists use maps to describe the location of a particular gene on a chromosome. One type of map uses the cytogenetic location to describe a genes position. The cytogenetic location is based on a distinctive pattern of bands created when chromosomes are stained with certain chemicals. Another type of map uses the molecular location, a…
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Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions
Background: Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes,i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accuracyof inference methods (Biller et al. in Genome Biol Evol 8:1427-39, 2016; Biller et al. in Beckmann A, Bienvenu L, JonoskaN, editors. Proceedings of Pursuit of the Universal-12th conference on computability in Europe, CiE 2016, Lecturenotes in computer science, vol 9709, Paris, France, June 27-July 1, 2016. Berlin: Springer, p. 35-44, 2016). In this line, wedefine a new genome rearrangement model called wDCJ, a generalization of the well-known double cut and join (orDCJ) operation that modifies both the gene order and the intergene size distribution of a genome.Results: We first provide a generic formula for the wDCJ distance between two genomes, and show that computingthis distance is strongly NP-complete. We then propose an approximation algorithm of ratio 4/3, and two exact ones:a
Supplementary table Species, systematic position and accession number of mitochondrial genome sequences used in the phylogenetic analysis and for gene order comparisons
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Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity
Nucleic Acids Res. 2013 Feb 1;41(3):1406-15. doi: 10.1093/nar/gks1286. Epub 2012 Dec 14. Evaluation Studies; Research Support, Non-U.S. Govt
«Collinearity» In geometry, collinearity is a property of a set of points, specifically, the property of lying on a single line. A set of points with this property is ...
Højst 1 isolat pr. salmonellaserovar pr. år fra samme epidemiologiske enhed må indgå i overvågningen. For æglæggende høner, slagtekyllinger og kalkuner udgør flokken den epidemiologiske enhed. For svin udgør bedriften den epidemiologiske enhed.. 2. Antal isolater, der skal testes. Antallet af salmonellaisolater, der skal indgå i overvågningen af antimikrobiel resistens pr. medlemsstat pr. år, er 170 for hver undersøgt population (dvs. æglæggende høner, slagtekyllinger, kalkuner og slagtesvin).. I medlemsstater, hvor der ved overvågnings- eller bekæmpelsesprogrammerne i et givet år tilvejebringes et lavere antal isolater end den tilstræbte stikprøvestørrelse, skal alle disse isolater indgå i overvågningen af antimikrobiel resistens.. I medlemsstater, hvor der tilvejebringes et højere antal isolater, indgår alle isolater eller et repræsentativt, tilfældigt udsnit, der mindst svarer til den tilstræbte stikprøvestørrelse.. 3. Test for antimikrobiel følsomhed. Som ...
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Following a spate of patient deaths in clinical trials testing modified T cells for the treatment of cancer, researchers work to reduce the treatments toxicity without sacrificing efficacy.. 0 Comments. ...
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In a landmark study, University of Otago researchers have achieved the feat of sequencing complete mitochondrial genomes for members of what was likely to be one of the first groups of Polynesians to settle New Zealand and have revealed a surprising degree of genetic variation among these pioneering voyagers.
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The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Cutler, E. B. 1994. The Sipuncula, their systematics, biology, and evolution. Cornell University Press, Ithaca, NY.. Cutler, E. B. and P. E. Gibbs. 1985. A phylogenetic analysis of higher taxa in the phylum Sipuncula. Systematic Zoology 34:162-173.. Edmonds, S. J. 2000. Phylum Sipuncula. Pages 375-400 in: Polychaetes & Allies: The Southern Synthesis. Fauna of Australia, vol. 4A, Polychaeta, Myzostomida, Pogonophora, Echiura, Sipuncula. P. L. Beesley, G.J.B. Ross, and C.J. Glasby, eds. CSIRO Publishing, Melbourne.. Ferrier, D. and P. W. H. Holland. 2001. Sipunculan ParaHox genes. Evol. Dev. 3:263-70 Huang, D. Y., J.-Y. Chen, J. Vannier, and J. I. Saiz Salinas. 2004. Early Cambrian sipunculan worms from southwest China. Proceedings of the Royal Society of London Series B 271(1549):1671-1676.. KennetLundin, K. and C.Schander. 2003. Epidermal ciliary ultrastructure of adult and larval sipunculids (Sipunculida). Acta Zoologica 84(2):113-119.. Maxmena, A. B., B. F. King, E. B. Cutler and G. Giribet. ...
Cutler, E. B. 1994. The Sipuncula, their systematics, biology, and evolution. Cornell University Press, Ithaca, NY.. Cutler, E. B. and P. E. Gibbs. 1985. A phylogenetic analysis of higher taxa in the phylum Sipuncula. Systematic Zoology 34:162-173.. Edmonds, S. J. 2000. Phylum Sipuncula. Pages 375-400 in: Polychaetes & Allies: The Southern Synthesis. Fauna of Australia, vol. 4A, Polychaeta, Myzostomida, Pogonophora, Echiura, Sipuncula. P. L. Beesley, G.J.B. Ross, and C.J. Glasby, eds. CSIRO Publishing, Melbourne.. Ferrier, D. and P. W. H. Holland. 2001. Sipunculan ParaHox genes. Evol. Dev. 3:263-70 Huang, D. Y., J.-Y. Chen, J. Vannier, and J. I. Saiz Salinas. 2004. Early Cambrian sipunculan worms from southwest China. Proceedings of the Royal Society of London Series B 271(1549):1671-1676.. KennetLundin, K. and C.Schander. 2003. Epidermal ciliary ultrastructure of adult and larval sipunculids (Sipunculida). Acta Zoologica 84(2):113-119.. Maxmena, A. B., B. F. King, E. B. Cutler and G. Giribet. ...
Shared synteny (also known as conserved synteny) describes preserved co-localization of genes on chromosomes of different species. During evolution, rearrangements to the genome such as chromosome translocations may separate two loci, resulting in the loss of synteny between them. Conversely, translocations can also join two previously separate pieces of chromosomes together, resulting in a gain of synteny between loci. Stronger-than-expected shared synteny can reflect selection for functional relationships between syntenic genes, such as combinations of alleles that are advantageous when inherited together, or shared regulatory mechanisms.[3]. The term is sometimes also used to describe preservation of the precise order of genes on a chromosome passed down from a common ancestor,[4][5][6][7] although many geneticists reject this use of the term.[8]. The analysis of synteny in the gene order sense has several applications in genomics. Shared synteny is one of the most reliable criteria for ...
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01: package com.mslv.oms.sample.atm_frame; 02: 03: import com.mslv.oms.automation.plugin.*; 04: import com.mslv.oms.automation.*; 05: import java.rmi.*; 06: import java.util.*; 07: import java.io.*; 08: import java.net.*; 09: import org.xml.sax.*; 10: import org.w3c.dom.*; 11: import javax.xml.parsers.*; 12: 13: public class UIMResponseHandler extends AbstractAutomator { 14: 15: public void run( String inputXML, AutomationContext task) 16: throws AutomationException { 17: try { 18: TaskContext tctx = (TaskContext)task; 19: String taskName = tctx.getTaskMnemonic(); 20: AtmFrameCatalogLogger.logTaskEventResponse 21: (taskName,tctx.getOrderId(),tctx.getOrderHistoryId(),inputXML); 22: 23: // Using the data returned from UIM, update the OSM order data 24: String updateXml = generateOMSUpdateString(inputXML); 25: tctx.updateOrderData(updateXml); 26: 27: // Complete the OSM task with the correct status 28: tctx.completeTaskOnExit( "success" ); } 29: 30: catch(OrderUpdateException ex) { 31: throw new ...
Listeria welshimeri ATCC ® 35897D-5™ Designation: Genomic DNA from Listeria welshimeri strain V8 TypeStrain=True Application:
Listeria welshimeri ATCC ® 35897D-5™ Designation: Genomic DNA from Listeria welshimeri strain V8 TypeStrain=True Application:
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