Allele genus analysis multilocus sequence typing. Medical search. Frequent questions

Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. (wikipedia.org)
In the final analysis step of MLST, the relatedness of isolates are made by comparing allelic profiles. (wikipedia.org)
The large number of potential alleles at each of the loci provides the ability to distinguish billions of different allelic profiles, and a strain with the most common allele at each locus would only be expected to occur by chance approximately once in 10,000 isolates. (wikipedia.org)
Alternatively, the relatedness of isolates can also be analysed with MultiLocus Sequence Analysis (MLSA). (wikipedia.org)
Molecular typing of 2 Burkholderia pseudomallei isolates suggests a link to Australian strains. (cdc.gov)
In capsular typing, the majority of the isolates were untypeable with prevalence of 52.15% and 43.58% in molecular and microbiological methods, respectively. (bvsalud.org)
If several different strains are present in a manufacturing facility - and this could easily be the case with many of the more common environmental isolates - investigation results may be misleading or inconclusive if strain typing and comparison have not been undertaken. (rapidmicrobiology.com)
16S sequencing is quite a flexible approach and sequencing the full 16S gene, rather than just the first 500 bp, provides additional data that is sometimes required for accurate species-level identification, but can also be useful for highlighting differences between bacterial isolates. (rapidmicrobiology.com)
MLST uses the sequences of internal fragments of seven essential, single-copy, housekeeping genes - i.e. genes required for processes that are essential for cell operation - to characterise isolates. (rapidmicrobiology.com)
It is generally undertaken by Sanger sequencing - in other words, the same sequencing technology used for 16S microbial identification of isolates. (rapidmicrobiology.com)
In recent years, advances in sequencing technology have led to what is known as "next-generation sequencing" becoming much more affordable and available, paving the way to whole genome sequencing of bacterial isolates as a more cost-effective means than MLST for comparing isolates of the same species, and this is now our preferred approach, for a number of different reasons. (rapidmicrobiology.com)
N. meningitidis isolates were evaluated for antibiotic susceptibility and characterised by whole genome sequencing. (bmj.com)
Genetic relationships among the meningococcal carriage isolates were determined using core genome multilocus sequence typing analysis. (bmj.com)
To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
The genetic homogeneity of ospC -A isolates was confi rmed agent, Borrelia burgdorferi , a spirochete that parasitizes by sequences at 6 additional chromosomal housekeeping vertebrates, is transmitted by hard-bodied ticks through- loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). (peerj.com)
According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. (researchsquare.com)
Our analysis includes the antimicrobial resistance profiles, the molecular characterization of the mechanisms of resistance to fluoroquinolones, virulence gene profiles and the molecular characterization of S. dysenteriae isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). (researchsquare.com)
Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. (biomedcentral.com)
The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. (biomedcentral.com)
CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. (biomedcentral.com)
To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. (biomedcentral.com)
Aspergillus spp include the most typical kinds separated through noninvasive type, whilst Mucorales tend to be TPCA-1 datasheet usually isolates through intense bacterial infections. (agckinases.com)
Those models are typing the false as us, strengthening the isolates. (ligaya-technologies.com)

Thus both the number and type of housekeeping genes interrogated by MLST may differ from species to species. (wikipedia.org)
However, before 2008 the genus was regarded as a single species named Enterobacter sakazakii which was subdivided into 8 phenotypes. (biomedcentral.com)
Until 2007 the Cronobacter genus was known as the single species Enterobacter sakazakii . (biomedcentral.com)
In conclusion, the analysis revealed a highly shared core genome among two Brucella species. (bvsalud.org)
These legumes include three species within two closely related genera Melilotus and Trigonella. (usda.gov)
They have a natural distribution extending from the Mediterranean basin through west Asia, where there is an unsurpassed number of species belonging to these genera. (usda.gov)
Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. (mdpi.com)
These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). (biomedcentral.com)
The genus Haemophilus includes 10 (sub)species that exclusively or predominantly colonize and infect humans [ 3 ]. (biomedcentral.com)
C), and Anisakis typica are the 4 major species of Anisakis type I larvae. (omicsdi.org)
Their species were analyzed using PCR-RFLP patterns and nucleotide sequences of internal transcribed spacers (ITS1, 5.8 subunit gene, and ITS2) and mitochondrial cytochrome c oxidase 2 (cox2). (omicsdi.org)
The genus consists of 2 genetically diverse species, C. immitis and C. posadasii , each of which contains 1 or more distinct populations with limited gene flow. (blogspot.com)
Coccidioides immitis and C. posadasii are the only 2 species recognized within the genus Coccidioides ( 1 ). (blogspot.com)
Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species. (peerj.com)
Although clinical microbiology typically relies on single-colony picks (which has the potential to underestimate species diversity and transmission events), within-host diversity of E. coli in the gut is crucial to our understanding of inter-strain competition and co-operation and also for accurate diagnosis and epidemiological analyses. (peerj.com)
Shigella is one of the major pathogens that causes diarrheal diseases in humans and animals.1,2 Since the first highly toxigenic species, Shigella dysenteriae, was isolated in 1898,3 four species has been described in Shigella genus, and each subgroup can be divided into multiple subtypes according to biochemical and serological properties. (researchsquare.com)
We use simulations to compare the statistical performance of Mongrail with that of an existing composite likelihood method (NewHybrids) and apply the method to analyze genome sequence data for hybridizing species of barred and spotted owls. (nfshost.com)
Development and characterization of microsatellite markers for genetic analysis of a Brazilian endangered tree species Caryocar brasiliense. (shengsci.com)
Gene flow, or introgression, refers to alleles from one species entering a different (and usually closely related) species through migration and hybridization. (biomedcentral.com)
Analysis of gene flow must take ILS into account, because both processes generate gene trees that are incongruent with the species tree. (biomedcentral.com)
Among the earliest methods to detect gene flow are a homoplasy-based analysis that finds taxa that are intermediate between putative parent species [ 9 ], and a gene tree comparison that identifies locus divergence younger than the species' divergence [ 10 ]. (biomedcentral.com)
Moreover, the lack of previous records of this species over the past century, together with the absence of lineage separation and the presence of relatively few private alleles, do not exclude the possibility of an even more recent colonisation event. (nature.com)
The elegant and original use of a probabilistic model of segregating alleles (implemented in the SEX-DETector method) allowed to identify both the sex and self-incompatibility loci [4], while this tool was initially developed for detecting sex-linked genes in species with strictly separated sexes (dioecy) [5]. (peercommunityin.org)
This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry. (biomedcentral.com)
The complete sequence of gyrA gene from 77 strains are reported in this study and analyzed in the context of publicly available sequences from N. meningitidis of other CCs as well as other Neisseria species. (biomedcentral.com)
Some clusters contain sequences from other Neisseria species. (biomedcentral.com)
Recombination within N.meningitidis strains and between Neisseria species was identified in SimPlot analysis. (biomedcentral.com)
This disease is caused by different species of apicomplexan parasites belonging to the genus Plasmodium . (biomedcentral.com)
The spectacled salamanders (genus Salamandrina) are endemic to the Apennine Peninsula and have diverged into two sibling species: S. terdigitata (in the south) and S. perspicillata (in the north), presumably in the late Miocene or early Pliocene. (uni-bielefeld.de)
By sequencing one mitochondrial (cytb) and two nuclear genes (RAG1 and POMC) and genotyping 10 microsatellite loci, we traced the evolution of these sibling species from their divergence to their contemporary population structure at a fine scale. (uni-bielefeld.de)
Using a multilocus coalescent-based approach, we estimated the temporal divergence of both species at approximately 2.25 mya (million years ago), which, hence, is much younger than previous estimates. (uni-bielefeld.de)
Hauswaldt JS, Angelini C, Gehara M, Benavides E, Polok A, Steinfartz S. From species divergence to population structure: A multimarker approach on the most basal lineage of Salamandridae, the spectacled salamanders (genus Salamandrina) from Italy. (uni-bielefeld.de)
From species divergence to population structure: A multimarker approach on the most basal lineage of Salamandridae, the spectacled salamanders (genus Salamandrina) from Italy", Molecular Phylogenetics and Evolution , vol. 70, 2014, pp. 1-12. (uni-bielefeld.de)
For example, anogenital warts are primarily caused by HPV6 (family Papillomaviridae , genus Alphapapillomavirus , species 10) [ 3 ], which brings a significant burden to both the healthcare system and patients. (biomedcentral.com)
The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. (omictools.com)
This refers to a particular nucleotide (or "base") in a DNA sequence that is variable within a species (or between related species). (panzea.org)
Yang (2008) re-identified the Lyuchun (previously transliterated as Luchun) population as a new species and transferred it to the genus Torrentophryne Yang, 1996, namely T. luchunnica Yang & Rao, 2008. (arphahub.com)
have produced data that suggest that the presence of Entamoeba- another gut-associated eukaryotic genus comprising multiple species of varying pathogencitiy-is strongly correlated with microbial composition and diversity. (blastocystis.net)

MLST directly measures the DNA sequence variations in a set of housekeeping genes and characterizes strains by their unique allelic profiles. (wikipedia.org)
Quoting Staphylococcus aureus as an example, seven housekeeping genes are used in MLST typing. (wikipedia.org)
For each of these housekeeping genes, the different sequences are assigned as alleles and the alleles at the loci provide an allelic profile. (wikipedia.org)
This does not use the assigned alleles, but instead concatenates the sequences of the gene fragments of the housekeeping genes and uses this concatenated sequence to determine phylogenetic relationships. (wikipedia.org)

Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. (bvsalud.org)
This study re-analyzed, using multi-locus sequence typing (MLST) and whole genome sequence with single nucleotide polymorphism analysis (WGS-SNP), 52 strains which had been identified as Enterobacter sakazakii as according to the convention at the time of isolation. (biomedcentral.com)
Bioinformatic analysis was then used to analyze the relatedness and global dissemination of these strains. (biomedcentral.com)
FusA allele sequencing revealed that 49/52 strains were Cronobacter sakazakii, while the remaining 3 strains were Escherichia coli, Enterobacter cloacae, and Franconibacter helveticus . (biomedcentral.com)
The C. sakazakii strains comprised of 8 sequence types (STs) which included the neonatal pathovars ST1, ST4 and ST12. (biomedcentral.com)
WGS-SNP analysis of the 32 C. sakazakii ST13 strains revealed 5 clusters and 5 unique strains which did not correlate with the country of product origin. (biomedcentral.com)
The WGS-SNP analysis demonstrated that indistinguishable Cronobacter strains within a sequence type can be unrelated, and may originate from multiple sources. (biomedcentral.com)
The use of WGS-SNP analysis to distinguishing of strains within a sequence type has important relevance for tracing the source of outbreaks due to Cronobacter spp. (biomedcentral.com)
In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. (bvsalud.org)
SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. (bvsalud.org)
The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. (bvsalud.org)
B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. (bvsalud.org)
SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. (bvsalud.org)
Strains are identified by comparing the sequence profiles obtained with previously published data. (rapidmicrobiology.com)
We used multilocus sequence analysis to estimate the genetic relatedness of 56 T. suavissima symbionts to 28 Ensifer reference strains. (usda.gov)
The strains also shared few alleles with Ensifer reference strains from other continents. (usda.gov)
We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. (biomedcentral.com)
Here we focus on the genotyping of Coccidioides strains from various origins by combining multiple studies in a meta-analysis and by using population genetics to clarify the causative agents of coccidioidomycosis. (blogspot.com)
We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
Drosophila melanogaster and D. simulans rescue strains produce fit offspring, despite divergent centromere-specific histone alleles. (shengsci.com)
Furthermore, the strains that are sharing the sequence of 4 or more genes (identified as a number for convenience) among the 7 genes used to determine STs could be classified into the same clonal complex (CC) [ 3 ]. (biomedcentral.com)

The principle of MLST is simple: the technique involves PCR amplification followed by DNA sequencing. (wikipedia.org)
The workflow of MLST involves: 1) data collection, 2) data analysis and 3) multilocus sequence analysis. (wikipedia.org)
Another approach that we have used in the past, is multilocus sequence typing (MLST). (rapidmicrobiology.com)
However, one of the issues with MLST is the cost of the sequencing required. (rapidmicrobiology.com)
Multilocus sequence typing (MLST) is the use of DNA dorferi ( 9 , 10 ). (cdc.gov)

While Sanger technology is well suited to sequencing part, or all, of a single gene, when multiplied up to the requirement to sequence seven distinct loci, it does become a more expensive option. (rapidmicrobiology.com)
Sequence data was partitioned according to the replicons upon which the loci are located. (usda.gov)
Here we obtained a well-resolved polymorphism type of intergenic spacer (IGS) sequence phylogeny of B. burgdorferi sensu stricto clonal complexes (corresponding to the ospC- A and -B groups) is associated by using multilocus sequence typing at housekeeping loci with hematogenous dissemination in patients with early as well as loci under adaptive evolution. (cdc.gov)
To evaluate the genetic diversity and population structure of I. lacunosa populations, we amplified inter-simple sequence repeats loci by polymerase chain reaction (ISSR-PCR) of 64 accessions using 14 ISSR primers for Ipomoea. (scirp.org)
Existing hybrid inference methods assume that alleles at different loci undergo independent assortment (are unlinked or in population linkage equilibrium). (nfshost.com)
Allele frequencies were estimated assuming (1) that genomic regions amplified by RAPD-PCR segregate as dominant alleles, (2) that genotypes at RAPD loci are in Hardy-Weinberg proportions, (3) identity in state (iis) among dominant amplified alleles and (4) iis among null alleles. (shengsci.com)
No linkage disequilibrium maintained through epistasis was detected among alleles at the 57 loci. (shengsci.com)
Using genomic library enrichment, the efficiency of SSR marker development was 14.4% from sequencing data to operationally useful loci. (shengsci.com)
Primer sequences for this set of 10 loci ar. (shengsci.com)
Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. (biomedcentral.com)
homozygotes for a single allele and heterozygotes therefore co-occur in natural populations at both sex and self-incompatibility loci [3]. (peercommunityin.org)
It will also be fascinating to study more finely the degree and extent of genomic differentiation at these two loci and to assess whether recombination suppression has extended stepwise away from the sex and self-incompatibility loci, as can be expected under some hypotheses, such as the sheltering of deleterious alleles near permanently heterozygous alleles [7]. (peercommunityin.org)
In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled). (biomedcentral.com)

Recent advances in DNA sequencing technologies have reduced sequencing costs and hands-on time, and whole-genome sequencing of bacterial pathogens is being routinely performed by public health organizations. (biomedcentral.com)

The analysis of genomic sequences by phylogenetic approaches can yield insights into evolutionary distances for 1000s of bacterial genomes. (biomedcentral.com)

In summary, the overarching rationale of SATURN was to improve methodological standards and conduct research that will help to better understand the impact of antibiotic use on acquisition, selection and transmission of AMR in different environments, by combining analyses of molecular, individual patient-level and ecologic data. (europa.eu)
Also, SATURN had as mission to improve methodological standards and conduct research to better understand the impact of antibiotic use on acquisition, selection and transmission of antibiotic-resistant bacteria (ARB) in different environments, by combining state-of-the-art analyses of molecular, ecologic and individual patient-level data. (europa.eu)
This prompted us to undertake this full-fledged molecular genetics study of anisakids from Kamchatka with phylogenetic reconstructions (NJ/ML) and calculated ranges of interspecific and intergeneric p-distances using ITS1-5.8S-ITS2 sequences. (omicsdi.org)
In this study, molecular analysis was performed on Anisakis larvae from the sea eels (Astroconger myriaster), the major source of human anisakiasis in Korea, collected from Tongyeong City, a southern coastal area of Korea. (omicsdi.org)
doi:10.1016/S0304-4017(03)00206-1 L. David Sibley / Veterinary Parasitology 115 (2003) 185-198 relationship is supported both by morphological comparisons (presence of sub-cortical alve-olar membranes) and by molecular analyses based on conserved protein sequences or smallsubunit (SSU) rRNA sequences. (pdfmedarticles.com)
2005. Molecular marker analyses of pistachio rootstocks by simple sequence repeats and sequence-related amplified polymorphisms. (agrifoodscience.com)
2002. Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. (agrifoodscience.com)
Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by Molecular Evolutionary Genetics Analysis version 6.0. (biomedcentral.com)
In the present study, a total of 99 accessions of Brassicaceae family, including 84 mustard (50 oilseed and 34 vegetable types) in China and 15 other Brassicaceae accessions were evaluated for their genetic diversity using nuclear and mitochondrial molecular markers. (mdpi.com)

To date, more than 250 HPV types have been identified and each of these genotypes are associated with infection at particular anatomical sites. (biomedcentral.com)

More recent studies have also suggested high rates of recombination within the Neisseria genus ( Didelot & Maiden, 2010 ). (peerj.com)

Methods: The Latin American Epidemiological Network of ALS (LAENALS) has been established to perform a comparative analysis of ALS epidemiology between three different Latin American populations (Cuba, Uruguay and Chile), and to test the hypothesis that the demographics, phenotype and outcome of ALS are influenced by ancestral origin, and that environmental and occupational risk factors differ across different ethnicities due to subtle differences in gene- environmental interactions. (cdc.gov)

Garnery L., Cornuet J.-M., and Solignac M. (1992) Evolutionary history of the honey bee ( Apis mellifera L.) inferred from mitochondrial DNA analysis, Mol. (apidologie.org)
Sequence variation in two regions of the mitochondrial ND1 gene, encompassing 710 base pairs, is described for 168 salmon from 11 rivers. (shengsci.com)
What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? (biomedcentral.com)

Bacterial meningitis can be caused by several types of bacteria including Streptococcus pneumonia or Neisseria meningitidis ( N.meningitidis ). (biomedcentral.com)

Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. (omictools.com)
In addition, we sequenced the full genome of a leucistic individual and obtained a highly-contiguous near-chromosome quality assembly of 1.69 Gb with an N50 of 14.5 Mb and an L50 of 29 sequences. (unige.ch)

New sequencing data are now routinely uploaded to public databases such as the Sequence Read Archives (SRA [ 6 ]), which provide ready access to extensive collections of sequencing data for many bacterial genera. (biomedcentral.com)
Sequences from specific bacterial pathogens are also available as curated collections of genomic assemblies bundled with their metadata together with dedicated tools for population genomic analyses. (biomedcentral.com)
One recent k -mer-based method, BIGSI, employs a data structure that stores a Bloom filter [ 11 ] of k -mers for each genome in a database, and can subsequently index and search very large databases of bacterial and viral sequences [ 12 ]. (biomedcentral.com)

J. C. Huang and M. Sun, "Genetic Diversity and Relationships of Sweet Potato and Its Wild Relatives in Ipomoea series Batatas (Convolvulaceae) as Revealed by Inter-Simple Sequence Repeat (ISSR) and Restriction Analysis of Chloroplast DNA," Theoretical and Applied Genetics, Vol. 100, No. 7, 2000, pp. 1050-1060. (scirp.org)

Nested analysis of variance indicated extensive genetic differentiation among locations within cities. (shengsci.com)

Results from nuclear and mtDNA sequences show that all Atlantic and Mediterranean populations belong to the same phylogroup, though microsatellite data indicate significant genetic divergence between the Azorean sample and all other locations, as well as among Macaronesian, western Iberian and Mediterranean regions. (nature.com)
The backbone in this type of research is the recognition that studies revealing a large contrast between the microbiomes of populations in developing countries and those of populations in urban industrialised areas have shown that geography is an important factor associated with the gut microbiome, but that such studies yet have to disentangle the effects of factors such as climate, diet, host genetics, hygiene and parasitism. (blastocystis.net)

Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. (biomedcentral.com)
Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. (biomedcentral.com)
However, given cases like Plethodon , there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses. (biomedcentral.com)
Given that many systematists routinely estimate phylogenies using combined mtDNA and nucDNA, we ask: what are the consequences of the common practice of combining these two types of data? (biomedcentral.com)

In the data collection step, definitive identification of variation is obtained by nucleotide sequence determination of gene fragments. (wikipedia.org)
The seven fragments sequenced are each approximately 450 - 500 base pairs long - so around the same length as the section of the 16S gene that we sequence for identification purposes. (rapidmicrobiology.com)
Approximately 10 µg of total DNA from the algal culture (ITS sequence GenBank JF831923) was used to construct a library (sheared DNA fragments were of 500 bp length) for 100 bp × 100 bp paired-end sequencing using an Illumina GAIIx and standard Illumina protocols (Illumina, San Diego, California, USA). (bioone.org)

The dominant sequence types were S. Give ST516 and S. Cotham ST617. (biomedcentral.com)

Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. (biomedcentral.com)
These approaches were implemented because k -mers can directly identify diverse genetic modifications such as single nucleotide polymorphisms (SNPs), insertions or deletions from short read sequences, and do not require assembled genomes or an explicit reference genome. (biomedcentral.com)
Furthermore, BIGSI was designed for dealing with genetically diverse collections of data, and other methods and different data structures might be more efficient for creating a query index of sequence data from closely related genomes. (biomedcentral.com)

For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)
In this chapter, we describe a complete pipeline of analysis, starting from (i) the integration of information from a reference set of experimentally studied systems, (ii) the identification of conserved proteins and the construction of their HMM protein profiles, (iii) the definition and optimization of "macsy-models," and (iv) their use and online distribution as tools to search genomic data for secretion systems of interest. (bvsalud.org)
Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. (omictools.com)

A huge set of data is produced during the sequencing and identification process so bioinformatic techniques are used to arrange, manage, analyze and merge all of the biological data. (wikipedia.org)

The phylogenetic analysis of CC4821 gyrA gene reveals at least 5 distinct genetic clusters. (biomedcentral.com)

At NCIMB, our microbial identification identifies bacteria by sequencing the first 500 bp of the 16S rRNA gene and searching for matches using the MicroSEQ database. (rapidmicrobiology.com)
Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. (biomedcentral.com)

BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. (biomedcentral.com)

A series of profiles can then be the identification marker for strain typing. (wikipedia.org)
CUPOhBa2127 marker has the highest allele number (Na=10). (agrifoodscience.com)
Each type of marker has its advantages and disadvantages. (panzea.org)
Although, in theory, each SNP marker can have up to four possible alleles (A, C, G, and T), in practice, only two alleles usually are present at any given SNP (e.g. (panzea.org)

2) a homomorphic diallelic self-incompatibility system acts in hermaphrodites, while such systems are usually multi-allelic, as rare alleles are advantageous, being compatible with all other alleles. (peercommunityin.org)

In the data analysis step, all unique sequences are assigned allele numbers and combined into an allelic profile and assigned a sequence type (ST). If new alleles and STs are found, they are stored in the database after verification. (wikipedia.org)
Similar to 16S rDNA sequencing, the development of this technique has been underpinned by online data sharing. (rapidmicrobiology.com)
Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. (biomedcentral.com)
Specifically, PrioriTree provides a suite of functions to generate input files for-and summarize output from-BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets. (nfshost.com)
This method is designed to be used on either one of two types of data: (1) sequence alignment where there is only one or a few samples per taxa, or (2) SNP data where the frequency of each allele in each population is known. (biomedcentral.com)
Approaches: A great LPA had been conducted making use of cross-sectional data from a non-treatment searching for neighborhood sample of females recruited after a police-reported event regarding IPV by way of a guy perpetrator (N_229), Nlultinomial regression analyses determined interactions among hidden account membership rights and also trauma-related evaluations. (agckinases.com)
Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. (biomedcentral.com)
How are topological conflicts between these data types typically resolved in the combined-data tree? (biomedcentral.com)

To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. (omictools.com)

2010. Study on genetic diversity of some Iranian Pistachio (Pistacia vera L.) cultivars using random amplified polymorphic DNA (RAPD), inter sequence repeat (ISSR) and simple sequence repeat (SSR) markers: A comparative study. (agrifoodscience.com)
Anacardiaceae) germplasm by RAPD analysis. (agrifoodscience.com)

Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. (biomedcentral.com)
We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. (omictools.com)

To strike the balance between the acceptable identification power, time and cost for the strain typing, about seven to eight house-keeping genes are commonly used in the laboratories. (wikipedia.org)
Here, we report the genome sequence of a Pasteurella multocida strain isolated from the heart blood of a spotted deer (Bareilly, India). (bvsalud.org)
Central databases have been established, to which users can submit strain information and new allele sequences. (rapidmicrobiology.com)
Conclusion: Diabetes mellitus is the most important influencing aspect BTK inhibitor with regard to sufferers using serious unpleasant way of sinusitis as well as the many concerned sinuses have been unilateral several sinuses along with maxillary nasal.Background: Numerous studies have utilised hidden course analysis ([CA) and also hidden profile evaluation ([PA) to look at posttraumatic strain dysfunction (PTSD) sign information in the selection of people. (agckinases.com)

HPV6 may be the most prevalent low risk alpha-papillomavirus type and is commonly associated with genital warts [ 2 ]. (biomedcentral.com)

The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. (biomedcentral.com)

The genus Anisakis sensu stricto should include Anisakis simplex sensu stricto , Anisakis pegreffii , Anisakis berlandi , Anisakis ziphidarum , and Anisakis nascettii . (omicsdi.org)

The Estimate multilocus function is when your software is proposed to wireless at your placed converter damn. (ligaya-technologies.com)

Population structure analysis determined three ancestral subgroups, with the majority of Arkansas and Mississippi accessions separated into two subgroups. (scirp.org)
These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. (peerj.com)
The unusual population structure of T. gondii originated within the last 10,000 years, while the genus itself is approximately 10 million years old. (pdfmedarticles.com)
Early work by O'Rourke & Stevens (1993) using electrophoretic analysis of enzymes of the pathogen and serological methods suggested that gonococci have a non-clonal sexual or panmictic population structure. (peerj.com)
5C+The%5C+result%5C+of%5C+surveying%5C+Population%5C+structure%5C+showed%5C+that%5C+there%5C+are%5C+two%5C+regeneration%5C+types%5C+which%5C+are%5C+seedlings%5C+and%5C+sprouts. (kib.ac.cn)

The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. (bvsalud.org)

Traditional phylogenetic analyses that assume a bifurcating tree fails to model complicated evolutionary processes such as incomplete lineage sorting (ILS), gene flow, and horizontal gene transfer [ 1 ]. (biomedcentral.com)

Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. (omictools.com)

Thus, the present study aimed to analyze E6 and E7 sequence variability among HPV6 isolated from cervical papilloma samples collected from patients in Southwest China. (biomedcentral.com)

The main disadvantage of SNPs is the small number of alleles typically present. (panzea.org)

Subsequent gene expression analyses reveal that all leucistic individuals that we analyzed exhibit a significantly decreased expression of MITF. (unige.ch)

Analysis of Nei's genetic distance (GD) values placed the accessions into four genotypic clusters, two of which were composed primarily of accessions from Arkansas and Mississippi with GD between clusters of 0.318. (scirp.org)
accessions by simple sequence repeat markers. (agrifoodscience.com)

Evidence for multilocus genetic control of preferential fertilisation in maize. (shengsci.com)
Microsatellites, in contrast, typically have numerous alleles (from 5 to 40 in maize Liu et al. (panzea.org)

used genotyping-by-sequencing to build a genome linkage map of P. angustifolia [4]. (peercommunityin.org)

A quite serious providence will be achieved in the cost and time that will occur with the preliminary analysis, and thus, the confusion that may occur in large scale orchard establishments or nurseries will be reduced to pretty low levels with DNA analysis. (agrifoodscience.com)

initiative trophiarum Typically is the mortality of an life energy by an analysis from the UK area, but the landscape has constrained to print superior. (liebherr-bhb.de)

Anatomy7

Organisms69

Diseases32

Chemicals and Drugs33

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes56

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture3

Information Science6

Named Groups1

Health Care13

Geographicals19

Isolates24

Species38

Housekeeping genes4

Strains21

MLST5

Loci13

Whole genome sequencing o1

Genomic sequences1

Molecular9

Genotypes1

Recombination1

Epidemiological1

Mitochondrial3

Neisseria1

Full genome2

Bacterial3

Applied Genetics1

Genetic differentiation1

Populations2

MtDNA4

Fragments3

Dominant1

Genomes3

Protein3

Bioinformatic1

Phylogenetic analysis1

Bacteria2

Nucleotide sequence1

Marker4

Advantageous1

Data8

20001

RAPD2

Algorithm2

Strain4

Commonly1

Mutation1

Sensu stricto1

Estimate1

Population5

Amplification1

Complicated evolutionary1

Virulence1

Variability among1

SNPs1

Gene expression1

Accessions2

Maize2

Linkage1

Occur1

Typically1