• There are several advantages associated with using 16S rRNA gene sequence as a biomarker in molecular characterization of bacterial endophytes because, these include its presence in all prokaryotes species, high variation across species and presence of many sequences of 16S rRNA from various organisms are present in the database and this gives reference sequences when identifying species [11]. (actascientific.com)
  • Moreover, we actually need near-complete SSU rDNA sequences (at least 1600 bp or so) to be able to infer robust phylogenetic relationships between reference sequences and sequences potentially reflecting new subtypes. (blastocystis.net)
  • Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. (peerj.com)
  • This pipeline is portable and reproducible across different computing environments, and flexible by allowing modifications to input parameters, assay primer and reference sequences. (cdc.gov)
  • Bacteria 16S ribosomal RNA gene, partial sequence. (nih.gov)
  • ClustalW alignment of Fsp25586, the obtainable partial sequence of the homologues serine protease Fsp23726, Fsp10953 and Fsp49256. (caspase1inhibitor.com)
  • Closest alignment was located with the partial sequence of 16S ribosomal RNA gene of F. nucleatum JCM 6328 subsp. (caspase1inhibitor.com)
  • In this study, we have sequenced, assembled and annotated transcriptome assemblies for the larvae of the above-mentioned pests. (biomedcentral.com)
  • This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. (biomedcentral.com)
  • However, the comparative transcriptome analysis of two spinach accessions with different bolting times identified genome-wide gene expression profiling and large-scale discovery of flowering-related genes from vegetative and reproductive leaves [ 13 ]. (biomedcentral.com)
  • We have also obtained transcriptome sequencing from total RNA submitted for gene expression analysis (NovoGene) of control and degenerating DLMs. (emerging-researchers.org)
  • Transcriptome sequencing revealed the presence of transcripts for Apolipophorin III identical to the published house cricket sequence and highly homologous for another cricket, Gryllus Bimaculatus. (emerging-researchers.org)
  • I helped review results for the transcriptome sequencing using NCBI blast and clustal alignment tools. (emerging-researchers.org)
  • The phylogenetic diversity of a population of 84 Beauveria strains -mainly B. bassiana (n = 76) - isolated from temperate, sub-tropical and tropical habitats was examined by analyzing the nucleotide sequences of two mt intergenic regions ( atp 6- rns and nad 3- atp 9) and the nuclear ITS1-5.8S-ITS2 domain. (biomedcentral.com)
  • Surprisingly, a BLAST search did not result in a close similarity with any published 16S RNA gene sequences from other bacteria. (wikipedia.org)
  • Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
  • Among the nTARs, 146 share significant similarity with proteins that have been identified in other species suggesting that they are hitherto unidentified genes in C. graminicola . (biomedcentral.com)
  • What is less easy is to set a 'one-fits-all' threshold for sequence similarity. (blastocystis.net)
  • BLAST analyses revealed two genes, CNAG_05233 and CNAG_07351, in C. neoformans which encode for proteins that have sequence similarity and domain conservation to the human NMD cofactors, hSmg5/7, and hSmg6, respectively, than to the yeast NMD cofactors, Ebs1p and Nmd4p, respectively. (rustbeltrna.org)
  • This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36 , without the level and length of similarity normally expected to support recombination. (biomedcentral.com)
  • FASTA - 'Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. (fenteany.com)
  • BLAST alignment results Siloam Karawaci Hospitals with samples were known to have 99 % similarity with Escherichia coli O157 H:7. (adoc.pub)
  • ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. (lu.se)
  • Though most chloroplast genes are believed to have been transferred to the nucleus during evolution, their genomes have maintained fairly conserved structures and gene contents throughout their evolutionary lineage 1 . (plos.org)
  • The cp genomes of land plants usually contain approximately 110-120 genes, which mostly participate in photosynthesis or gene expression 4 , 5 . (plos.org)
  • Long read sequencing offers new opportunities for metagenomics studies, especially the ability to generate reads overlapping conserved or complex genomic regions which often fragments metagenome-assembled genomes when using short-reads. (merenlab.org)
  • Apart from a typical gene content and organization, the Beauveria mt genomes contained several introns and had longer intergenic regions when compared with their close relatives. (biomedcentral.com)
  • In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. (biomedcentral.com)
  • To quantify the overall extent of HGT in plastid genomes, we searched exhaustively for HGT among the 42 sequenced plastid genomes available when this study began. (biomedcentral.com)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • A total of 69, 862, 281 base pair clean reads were assembled into 61, 627 high-quality unigenes, of which 41, 591 (67.5%) and 39, 297 (63.8%) were aligned in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), respectively. (rhhz.net)
  • Angiosperm mitochondrial genomes also contain numerous introns, some of which have been split such that the resulting gene fragments must be transcribed separately and then trans- spliced together [ 7 ]. (biomedcentral.com)
  • Plant mitochondrial genomes contain genes for their own rRNA subunits as well as for some of the ribosomal proteins and tRNAs required for translation (Figure 1 ), but many necessary ribosomal protein and tRNA genes are located in the nuclear genome, so their gene products must be imported into the mitochondrion [ 15 ]. (biomedcentral.com)
  • Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). (spandidos-publications.com)
  • Molecular characterization using PCR based, small subunit ribosomal r RNA (SSU-rRNA) gene analysis was carried out in order to establish the spore identity and to derive phylogenetic relationships among the key isolates. (longdom.org)
  • The SSU-rRNA gene sequence homology was analysed using BLAST, which placed, six of our spore isolates in the genus of Nosema except spore isolate: VIK-52 Pr that was clustering along with the genus of Vairimorpha. (longdom.org)
  • Five isolates of endophytic strains which were displayed the strongest antibacterial and antioxidant activities were identified based on ribosomal RNA (rRNA) gene sequence analysis. (ui.ac.id)
  • Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. (scielo.br)
  • If you do not check for chimeras, you might end up including chimeric DNA sequences in your phylogenetic analyses that will distort and confuse the interpretation and - in the worst case - lead to erroneous calling of new subtypes. (blastocystis.net)
  • Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. (frontiersin.org)
  • The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. (biomedcentral.com)
  • Our search relied primarily on phylogenetic analyses, but also involved scrutiny of each potential case (including generation of new gene sequences from phylogenetically relevant taxa) to rule out artifacts and various types of homoplasy. (biomedcentral.com)
  • place determination of stingless bees sampling, sampling, and molecular identification (DNA extraction, DNA amplification, and sequencing), followed by the data analysis using NCBI database and MEGA X software. (ugm.ac.id)
  • A simple BLAST query in GenBank (NCBI Database) should tell you whether your sequence is Blastocystis or something else. (blastocystis.net)
  • Biswal D, Konhar R, Debnath M, Parameswaran S, Sundar D, Tandon P. Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India. (plos.org)
  • Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. (plos.org)
  • Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
  • Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata , respectively. (biomedcentral.com)
  • 10,200 protein-encoding genes were predicted based on the genome sequence. (springeropen.com)
  • The genes and proteins were predicted and annotated based on the genome sequence. (springeropen.com)
  • In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia . (biomedcentral.com)
  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, rpoB, parC and ftsY sequences of strain B20 are GQ857549, GQ983049, GQ983050, and GU289825, respectively. (wikipedia.org)
  • 3] In fact a quick BLAST search of Propionibacterium acnes genes for 16S ribosomal RNA (GenBank: AB097215.1) against M. tuberculosis shows an 88% identity within the first 100 hits. (j-alz.com)
  • Comparative 16S rRNA gene sequence analysis showed that this strain belongs to the family Coxiellaceae, order Legionellales of Gamma-proteobacteria, and the closest relatives are different Rickettsiella spp. (wikipedia.org)
  • This research aims at detecting bacterial pathogens that cause diarrhea by the method of polymerase chain reaction (PCR), using 16S rRNA gene sequence analysis. (adoc.pub)
  • The evidence of infection was further reconfirmed by using PCR-assay, thus established its role as a human pathogen and later whole genome sequencing was performed. (wikipedia.org)
  • The reproducibility, flexibility, analysis automation, and improved sequence resolution of the MPAS pipeline make it well suited for a high throughput tick pathogen surveillance program. (cdc.gov)
  • NMD targets mRNAs which possess premature termination codons (PTCs) resulting from DNA damage, RNA damage, transcriptional errors, or PTCs programmed into the mRNA sequence. (rustbeltrna.org)
  • A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome‑wide transcriptional sequencing was performed. (spandidos-publications.com)
  • MicroRNAs (miRNAs or miRs) are involved in the post-transcriptional regulation of gene expression via complete or partial base pairing with the 3′untranslated region of target genes ( 3 ). (spandidos-publications.com)
  • The fungal ITS sequences are a RefSeq Targeted Loci BioProject ( PRJNA177353 ). (nih.gov)
  • by using multilocus sequence typing (MLST) and The patient with Tsukamurella infection was an whole-genome sequencing (WGS) ( 2 ). (cdc.gov)
  • Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. (bvsalud.org)
  • An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. (biomedcentral.com)
  • This will lay the foundation for genomic and transcriptomic resources for these pest species, which can be utilized to develop methods of pest control in Brassica napus , such as host-induced gene silencing (HIGS) technology and spray-induced gene silencing (SIGS). (biomedcentral.com)
  • With the development of next-generation sequencing (NGS), research has focused on comprehensive genomic analysis based on tumor molecular features, such as somatic mutations and copy number variation. (spandidos-publications.com)
  • The bacteria are non-motile, and 16S rRNA, rpoB, parC and ftsY gene sequencing indicate that this bacterium is clearly different from all other recognized species. (wikipedia.org)
  • uncultured bacterium nitrogenase reductase (nifH) gene, partial cds. (nih.gov)
  • Large-scale genomics and transcriptomics approaches have been proven to enable the identification of pathogenicity genes in fungi affecting humans or plants [ 8 ], which makes them valuable tools towards a better understanding of fungal infection mechanisms. (biomedcentral.com)
  • This post is geared toward fungi researchers as well as RefSeq and BLAST users. (nih.gov)
  • To address these issues, Conrad Schoch, NCBI's fungi taxonomist, and Barbara Robbertse, NCBI's fungi RefSeq curator, in collaboration with outside mycology experts, are curating a set of fungal sequences from internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA genes. (nih.gov)
  • Amplicon or PCR product was analyzed by sequencing method to determine the DNA sequence. (ui.ac.id)
  • Here is a table to summarize the three HMW DNA extraction methods, their replicates, variants, and also the additional sample used for amplicon and short-read sequencing. (merenlab.org)
  • To determine if such co-infections were overlooked particularly in ticks infected with Bbss, we retested and analyzed a subsample of 845 Borrelia infected ticks using a next generation sequencing multiplex PCR amplicon sequencing (MPAS) assay that can identify Borrelia species and Bbsl co-infections. (cdc.gov)
  • A recently developed next generation sequencing (NGS) targeted multiplex PCR amplicon sequencing (MPAS) assay has enhanced the detection capabilities for Ixodes-associated human pathogens found in Ixodes scapularis and Ixodes pacificus ticks compared to the routinely used real-time PCR assay. (cdc.gov)
  • We describe the development and validation of the MPAS pipeline, a bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay. (cdc.gov)
  • The distributional patterns of microbial genes suggested Dead Sea community trends in mono- and divalent cation metabolisms as well as in transposable elements. (nature.com)
  • 12 conserved signature indels (CSIs) were also identified for this clade in the proteins inositol monophosphatase, lysyl-tRNA synthetase, elongation factor P-(R)-beta-lysine ligase, tol-Pal system beta propeller repeat protein TolB, FKBP-type peptidyl-prolyl cis-trans isomerase, response regulator transcription factor, 30S ribosomal protein S2, glycine cleavage system aminomethyltransferase GcvT, M3 family metallopeptidase, lysm peptidoglycan-binding domain-containing protein and oligopeptide transporter. (wikipedia.org)
  • ATP-binding cassette (ABC) transporter proteins were up-regulated during the entire response phase, and genes involved in glycerophospholipid metabolism were up-regulated during the late phase of the Mn response. (rhhz.net)
  • ClustalW - '[A] general purpose multiple sequence alignment program for DNA or proteins. (fenteany.com)
  • As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. (biomedcentral.com)
  • ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
  • Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. (biomedcentral.com)
  • We tested six HMW DNA extractions, but only three were able to generate enough DNA yield and purity to match the requirements for MinION sequencing. (merenlab.org)
  • I performed the dissections, the RNA extractions, helped design and order primers, performed both RT-PCR and Real-time PCR. (emerging-researchers.org)
  • Rossen said this about species identification (such as the species P. acnes ) using next generation sequencing: "when one gets down to the species level such molecular methods need "a priori" knowledge of the likely pathogenic species that could be present in the sample" [5]. (j-alz.com)
  • This set of standard DNA sequences for fungal taxa not only addresses these difficulties in identifying and classifying fungal species by morphology, but is also essential for analyzing environmental (metagenomics) sequencing studies. (nih.gov)
  • The curated ITS sequences, described in a recent article in Database ( PMC Free Article ), all have associated specimen data and, when possible, are taken from sequences from type materials, ensuring correct species identification and tracking of name changes. (nih.gov)
  • Nine 16S rRNA amplicons out of twenty-four were sequenced and species were identified as Izhakiella capsodis, Escherichia fergusonii, Shigella dysenteriae, Xernorhabdus szentirmaii, Providencia rettgeri, Dickeya zeae and Escherichia albertii . (actascientific.com)
  • Using KEGG database it was discovered that sequenced species have potential to produce antibiotics such as fosfomycin and streptomycin. (actascientific.com)
  • Also, that the 16S rRNA gene can be used to identify species. (actascientific.com)
  • The present study recorded that a difference in the sequence of nitrogen base appears on the characteristics of the species in terms of the composition of the cuticle of the parasites species although many classifications have kept it within the same species. (vetmedmosul.com)
  • DNA sequence chimeras are sequences where one piece of DNA is combined with a piece of DNA from another strain/species/genus/etc., which can happen during PCR-based amplification of DNA. (blastocystis.net)
  • Most, if not all of these transfers seem to be the result of a gene being transferred from the mitochondrial genome of one species to that of another. (biomedcentral.com)
  • Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
  • Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. (biomedcentral.com)
  • To better understand the geographic distribution and vector associations of Bbsl spirochetes in frequent and infrequent human-biting Ixodes species ticks in the US, we previously screened 29,517 host-seeking I. scapularis or I. pacificus ticks and 692 ticks belonging to eight other Ixodes species for Borrelia spirochetes using a previously described tick testing algorithm that utilizes a combination of real-time PCR and Sanger sequencing for Borrelia species identification. (cdc.gov)
  • The MPAS pipeline identified the same number of positive ticks for Anaplasma phagocytophilum and Babesia species as the original analysis, but the MPAS pipeline provided enhanced sequencing resolution of Borrelia burgdorferi sensu lato co-infected samples. (cdc.gov)
  • Genes that were differentially expressed during Mn response and recovery belong to several dominant KEGG pathways. (rhhz.net)
  • Genes in the phenylpropanoid pathway were differentially expressed in the repair process after Mn treatment. (rhhz.net)
  • Gene sequence analysis indicated that this is the second documented case of infection with Acanthamoeba spp. (biomedcentral.com)
  • Identification was performed by sequencing 18S rRNA that was compared with known genes using Blast search in the combination of phylogenic analysis by using Clustal W and PhyML in GenomeNet. (microbiologyjournal.org)
  • in this case, the goal is to collect and curate fungal sequences from targeted loci - specific molecular markers such as protein coding or ribosomal RNA genes used for phylogenetic analysis. (nih.gov)
  • The aim of the study was to provide in-depth analysis of fungal communities associated with the skin (outer part) and mesocarp (inner fleshy part) of stored dates ( Tamar ) of two cultivars ( Khenizi and Burny ) through the use of Illumina MiSeq sequencing. (biomedcentral.com)
  • Epigenetic analysis revealed a specific N 6 -methyl adenine (m 6 A) methylating pattern including methylation of alginate, flagellar and quorum sensing associated genes. (frontiersin.org)
  • Differential gene expression analysis indicated that this isolate formed excessive biofilm by reducing flagellar formation (7.4 to 1,624.1 folds) and overproducing extracellular matrix components including CdrA (4.4 folds), alginate (5.2 to 29.1 folds) and Pel (4.8-5.5 folds). (frontiersin.org)
  • Network analysis pinpointed several well-known flowering-related genes such as ELF , COL1 , FLT , and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. (biomedcentral.com)
  • The amplification product was submitted for DNA sequence analysis and the sequence was compared (98% identity) to published gene records using the NIH MegaBlast analysis tools. (emerging-researchers.org)
  • Preliminary analysis focused on ovary and DLM tissue suggests that apolipophorin and ribosomal RNA are expressed by each tissue. (emerging-researchers.org)
  • The automation of the summary report, BLAST report, and phylogenetic analysis reduces the amount of time needed for downstream analysis. (cdc.gov)
  • Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. (biomedcentral.com)
  • In order to clarify the biological and pharmacological mechanisms of O. sinensis , we carried out the genome sequencing of H. sinensis, anamorph of O. sinensis , for the first time, described the annotation and gene expression, and analyzed the complete sequencing data (Li et al. (springeropen.com)
  • It's still common practice to amplify and sequence only about 1/3 of the SSU rRNA gene and use that as a taxonomic identifier. (blastocystis.net)
  • Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. (biomedcentral.com)
  • mosquitoes in Marsabit and Turkana Counties by using endpoint PCR and morphological and sequence identification. (cdc.gov)
  • RNA-Seq offers the potential for substantially improved gene annotations and for the identification of posttranscriptional RNA modifications, such as alternative splicing and RNA editing. (biomedcentral.com)
  • The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
  • Molecular Toolkit - Utilities to analyze and manipulate nucleic acid and protein sequences. (fenteany.com)
  • Gene expression also relies on extensive C-to-U (and sometimes U-to-C) RNA editing, in which substitution of specific pyrimidines in the mRNA sequence restores phylogenetically conserved codons [ 8 ]. (biomedcentral.com)
  • In addition, Mollerup's 2016 Journal of Clinical Microbiology review regarding P. acnes , using similar next-generation sequencing as the Bristol group, cautioned: "Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. (j-alz.com)
  • Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. (peerj.com)
  • However, three genes - clpP , ycf2 , and rpl36 - provided strong support for taxa moving far from their organismal position. (biomedcentral.com)
  • Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. (biomedcentral.com)
  • The evidence found thus far for HGT to the plastid proceeded from studies of a particular gene or intron. (biomedcentral.com)
  • 2014. Molecular phylogeny of Malaysian stingless bee (Hymenoptera: Apidae: Meliponini) revealed using partial 16s rRNA mitochondrial gene. (ugm.ac.id)
  • 2003. Molecular phylogeny of the stingless bees (Apidae, Apinae, Meliponini) inferred from mitochondrial 16S rDNA sequences. (ugm.ac.id)
  • The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms. (biomedcentral.com)
  • The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. (biomedcentral.com)
  • These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage. (biomedcentral.com)
  • 1) "native" tRNAs encoded in the mitochondrial genome and inherited from the α-proteobacterial progenitor of mitochondria, 2) chloroplast-like tRNAs, which are also encoded in the mitochondrial genome but which were acquired by functional gene transfer from the chloroplast genome during land plant evolution, and 3) nuclear-encoded tRNAs imported from the cytosol. (biomedcentral.com)
  • The ensuing solution was sequenced (gene lender accession quantity KM023647) and blasted from the National Middle for Figure four. (caspase1inhibitor.com)
  • Design and test primers for this sequence using Primer-BLAST. (nih.gov)
  • Nine nuclear and four cytoplasmic genes were appropriate to design thirteen specific primers based on their nucleotide polymorphism. (ijpp.ir)
  • ITS-MF1 and ITS-MR2 (ITS-M2 set, from internal transcribed spacers of rRNA gene) were selected as the most efficient primers based on their specificity and sensitivity. (ijpp.ir)
  • Gene specific primers were designed based on the published sequence for Acheta domesticus Apolipophorin III, and PCR amplification was performed to assess the presence of transcripts for Apolipophorin III in the cDNA derived from the tissues. (emerging-researchers.org)
  • Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. (bvsalud.org)
  • The data provide information on larval physiology and form a basis to develop highly specific RNA interference-based plant protection. (biomedcentral.com)
  • Amino acid sequences of the putative serine protease open up studying frames FN1426 (Fsp25586) (A), and FNV0835 (Fsp49256) (B). Crimson emphasize signifies sequences recognized by mass spectrometry of the ninety nine kDa serine protease of F. nucleatum ATCC 25586 (A), and of the fifty five kDa serine protease of F. nucleatum ATCC 49256 (B). doi:10.1371/journal.pone.0111329.g003 DNA was isolated from F. nucleatum ATCC 25586 as explained above. (caspase1inhibitor.com)
  • CBS Prediction Servers - Nucleotide and amino acid sequence-based bioinformatics tools for structure and function prediction. (fenteany.com)
  • Accordingly, 16S rRNA gene sequencing (16S-seq) and bulk immune repertoire sequencing (IR-seq) were performed to characterize GM and intrahepatic TCR IR. (frontiersin.org)
  • The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. (biomedcentral.com)
  • The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. (peerj.com)
  • With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. (peerj.com)
  • A fundamental step in such studies is to predict the taxonomy of sequences found in the reads. (peerj.com)
  • The Department of Biotechnology (DBT), Government of India, funded this work under the DBT-NER Twinning program "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" (Grant ID BT/325/NE/TBP/2012 dated August 07, 2014). (plos.org)
  • Northern blot assessment of the ribosomal protein transcript, RPL2, also demonstrated slower decay of homeostatic transcripts in the upf1 Δ mutant following oxidative stress. (rustbeltrna.org)
  • Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. (biomedcentral.com)
  • Sequence alignment of fusolisin. (caspase1inhibitor.com)
  • The result of sequencing DNA then compared with GenBank’s database using Basic Local Alignment Search Tool (BLAST). (ui.ac.id)
  • But if you look carefully at the alignment of the query sequence and the reference sequence, you'll probably note that a large part of the sequence aligns very well to the most similar reference sequence, while a minor part of it has great dissimilarity. (blastocystis.net)
  • BLAST @ EBI - Perform BLAST (Basic Local Alignment Search Tool) searches. (fenteany.com)
  • This result was followed by sequencing and alignment of data on Basic Local Alignment Search Tool (BLAST). (adoc.pub)
  • Hasil ini dilanjutkan dengan sekuensing dan penyejajaran data pada Basic Local Alignment Search Tool (BLAST). (adoc.pub)
  • The purpose of this page is to provide access to reproducible data products that underlie our key findings in the study " High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes " by Trigodet & Lolans et al. (merenlab.org)
  • A study that benchmarks six high molecular weight DNA extraction strategies (commercially available kits, phenol-chloroform extraction, and agarose encasement followed by agarase digestion) for long-read sequencing of metagenomes with MinION. (merenlab.org)
  • Some of the enzymes which generate aromatic radicals that break down most prominent bacterial strains found were isolated and tax- the complex linkages present in lignin to compounds of lower onomically identified using 16S ribosomal RNA (rRNA) se- molecular weight. (lu.se)
  • Mt sequences allowed better differentiation of strains than the ITS region. (biomedcentral.com)
  • We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)
  • In response to Mn toxicity, genes were expressed in twelve distinct patterns, which can be divided into four general categories: initial, stable, dose-dependent, and lineage. (rhhz.net)
  • siRNA Database - [A] comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms. (fenteany.com)
  • Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. (bvsalud.org)
  • Phylogeny of the Cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data. (nih.gov)
  • Most section will require the reader to create a tab delimited files with the name of samples and path to the appropriate data (raw sequences, assemblies). (merenlab.org)
  • BodyMap - An anatomical expression database of human genes. (fenteany.com)
  • FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. (spandidos-publications.com)
  • The European Ribosomal RNA Database - Ribosomal RNA (rRNA) sequence data listed by organism, secondary structure prediction programs and other software, links to related sites. (fenteany.com)