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Consensus SequenceMolecular Sequence DataBase SequenceConsensusAmino Acid SequencePromoter Regions, GeneticBinding SitesCloning, MolecularTranscription, GeneticSequence Homology, Nucleic AcidSequence AlignmentSequence Homology, Amino AcidDNADNA-Binding ProteinsTranscription FactorsConsensus Development Conferences as TopicProtein BindingCell LinePlasmidsSequence Analysis, DNAMutationEscherichia coliRestriction MappingMutagenesis, Site-DirectedRegulatory Sequences, Nucleic AcidRNA, MessengerIntronsRepetitive Sequences, Nucleic AcidDNA PrimersBacterial ProteinsGene Expression RegulationGenes, BacterialInterferon Regulatory FactorsGenesDNA, ComplementaryRecombinant Fusion ProteinsTransfectionPolymerase Chain ReactionRecombinant ProteinsDNA, BacterialConserved SequenceNucleic Acid ConformationRepressor ProteinsVirus InternalizationHeLa CellsExonsRNA SplicingProtein Structure, TertiaryOligodeoxyribonucleotidesAmino Acid MotifsGene Expression Regulation, BacterialOperonElectrophoretic Mobility Shift AssayNuclear ProteinsSequence DeletionPhylogenySubstrate SpecificitySaccharomyces cerevisiaeEnhancer Elements, GeneticModels, MolecularGene LibraryDNA, FungalChloramphenicol O-AcetyltransferaseGenes, RegulatorKineticsChromosome MappingSequence AnalysisPhosphorylationDelphi TechniqueCells, CulturedCarrier ProteinsPeptidesDNA Mutational AnalysisDNA Restriction EnzymesOpen Reading FramesResponse ElementsProtein ConformationOligonucleotide ProbesGenes, ReporterTrans-ActivatorsGlycosylationDNA FootprintingStructure-Activity RelationshipDeoxyribonuclease IZinc FingersTranscriptional ActivationCricetinaeDNA Transposable ElementsRNAProtein BiosynthesisPeptide FragmentsNucleotide MappingMutagenesisCell NucleusPoint MutationDNA, ViralBlotting, NorthernMembrane ProteinsGene ExpressionRNA, Viral
GenomeGenesGenomesHigh-throughputCDNANucleicSplice sitesChIP-SeqSimilarityGenomicSwissProtMRNADataMotif discoveryViralProteinsMotifsLengthsGene expressionGeneratesPutativeTranscriptionCodonRibosomal2023HttpsConsistsRepresentsFacilitateResultsReceptorsProteinNext-generationExpressionVariationProductsCellDeliversJournalFoundCompleteMechanismsAnalysisDatabaseAbstractSitesReferenceBaseBlock
Genome13
  • Note 1 to entry: Gene editing is a subclass of genome editing ( 1.2 ). (nist.gov)
  • We compared the whole genome sequences of 39 AHS viruses (AHSVs) from field AHS cases to determine the source of 3 such outbreaks. (cdc.gov)
  • In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. (biomedcentral.com)
  • We present a novel genome sequencing strategy, which is useful when evolutionary diversity is the question of interest. (biomedcentral.com)
  • When the background expectation is similarity, how does one use low coverage genome sequencing to detect that which makes organisms distinct? (biomedcentral.com)
  • These kits are single-box solutions for sequencing the entire viral genome. (qiagen.com)
  • The kits include reagents to reverse transcribe the RNA into cDNA, primers to specifically enrich for the viral genome and Unique Dual Indices (UDIs) for sequencing. (qiagen.com)
  • The QIAseq DIRECT SARS-COV-2 Kit is a single-box solution for generating whole genome libraries that are sequencing-ready and compatible with all Illumina platforms. (qiagen.com)
  • Viruses consist of nucleic acid (viral genome) and a limited number of proteins that facilitate entry into a host cell, replication of the genome and production of virions. (qiagen.com)
  • Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. (darkenergybiosphere.org)
  • The oral, nasal and fur swabs for both pets tested positive for SARS-CoV-2 by qRT-PCR and consensus whole-genome sequences from the dog and cat were 100% identical and matched the B.1.1.7 VOC. (rcvsknowledge.org)
  • Data from COVID-19 case investigations, contact tracing, the Commonwealth's immunization registry and whole genome sequencing were collated and analysed as part of this study. (who.int)
  • A genome sequence of 189,344 bp encoding 166 open reading frames (ORFs) was obtained. (cdc.gov)
Genes4
  • Curved links encode sequence similarity and outer data tracks represent consensus similarity statistics and orthologous genes. (bcgsc.ca)
  • Here, we show that c-Myc induction during cell cycle entry leads to a transient decrease in Mnt-Max complexes and a transient switch in the ratio of Mnt-Max to c-Myc-Max on shared target genes. (silverchair.com)
  • For comparison, the corresponding wild type genes were subcloned using native sequences available from the NCBI database. (thermofisher.com)
  • Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. (cdc.gov)
Genomes3
  • The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. (bcgsc.ca)
  • Sequence data can be used to identify variants across different samples, as well as to compare with multiple genomes - from consensus reference genomes to one of many genomes that have been uploaded from around the world. (qiagen.com)
  • A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Quebec, Canada In April 2020, the Coronavirus Sequencing in Québec (CoVSeQ) consortium was assembled to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and transmission within the province. (computationalgenomics.ca)
High-throughput3
  • In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. (nature.com)
  • Scasa, an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. (ne.jp)
  • C3G Bioinformatics Platform at the Rosalind and Morris Goodman Cancer Institute With next-generation sequencing and other high-throughput technologies revolutionizing life sciences and health care research, data processing and interpretation, rather than data production, has become the major limiting factor for discovery and innovation. (computationalgenomics.ca)
CDNA2
  • The M. truncatula EST database used in this study contained 140,000 sequence entries from 30 non-normalized cDNA libraries representing a set of vegetative and reproductive organs. (biomedcentral.com)
  • Sequencing of cDNA obtained from reverted virions revealed mutations in E1 (I262L) and E2 (N415D). (monash.edu)
Nucleic3
  • The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. (wikipedia.org)
  • They are \citep{schneider1990} and \citep{yu1995} \bibliography{tex} \bibliographystyle{plainnat} \end{document} tex.bib file: @article{schneider1990, author = 'Schneider T.D.and Stephens R.M.', title = '{Sequence Logos: A New Way to Display Consensus Sequences}', journal = 'Nucleic Acids Res. (tug.org)
  • Because of degeneracy, one protein can be encoded by many alternative nucleic acid sequences. (thermofisher.com)
Splice sites1
  • The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. (rcsb.org)
ChIP-Seq2
  • De novo motif discovery, i.e. discovery of potentially novel motifs from a set of DNA sequences, can work well for input sequences with high motif content, like from ChIP-Seq experiments. (biomedcentral.com)
  • de novo generated motifs, by analyzing ChIP-seq/-exo sequences using a custom motif discovery pipeline (check the code at our repository ). (genereg.net)
Similarity1
  • The sequence similarity among these different repeats or domains is low, however they exhibit considerable structural similarity. (eu.org)
Genomic3
  • Kozak discovered the sequence through a detailed analysis of DNA genomic sequences. (wikipedia.org)
  • Low coverage sequencing is now a routine strategy to uncover functional or 'constrained' genomic elements [ 30 ]. (biomedcentral.com)
  • We report the complete genomic coding sequence of the Georgia 2007/1 isolate and comparison with other isolates. (cdc.gov)
SwissProt4
  • SwissProt sequences and OMIM curated human diseases associated with missense mutations within the LRR_TYP domain. (embl.de)
  • The tool's input is a column which holds either an Ensembl gene or transcript ID, a Consensus CDS ID, or a protein ID from either Ensembl or UniProt/SwissProt. (eurac.edu)
  • Uniprot/SwissProt entries are curated forms of UniProt/TrEmbl entries, so they mutually exclude each other and cannot be mapped to each other. (eurac.edu)
  • Mapping entities is generally only possible between blocks, as Mapping between TrEmbl or SwissProt entries (accession number to entry name and vice versa) is possible, though. (eurac.edu)
MRNA4
  • Kozak sequence strength refers to the favorability of initiation, affecting how much protein is synthesized from a given mRNA. (wikipedia.org)
  • The A nucleotide of the "AUG" is delineated as +1 in mRNA sequences with the preceding base being labeled as −1. (wikipedia.org)
  • Once the PIC binds to the mRNA it scans until it reaches the first AUG codon in a Kozak sequence. (wikipedia.org)
  • Our GeneOptimizer algorithm enables true multiparametric optimization, dealing with a large number of sequence-related parameters involved in different aspects of gene expression, such as transcription, splicing, translation, and mRNA degradation. (thermofisher.com)
Data7
  • Here, we report computational and comparative analyses of survey sequence data to address the question of diversity. (biomedcentral.com)
  • What data does each entry hold? (genereg.net)
  • However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. (darkenergybiosphere.org)
  • Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. (darkenergybiosphere.org)
  • In the future, we will see the stack broken down into data availability and consensus, block verification & building, transaction sequencing & block proposing, and general-purpose or application-specific compute. (theblock.co)
  • Ethereum's most promising scalability solutions all address some areas or combinations of the stack: Sharding addresses data availability, consensus and block building while Rollups allow transactions to be processed on layer 2 with security tied to layer 1 through validity or fraud proofs. (theblock.co)
  • The CAPI system is programmed with built-in consistency checks to reduce data entry errors. (cdc.gov)
Motif discovery1
  • This makes them hard to discover with de novo motif discovery methods since the signal-to-noise ratio can be quite low when searching for motifs embedded in long background sequences. (biomedcentral.com)
Viral1
  • To investigate the emergence of compensatory mutations in the viral proteins during cell passaging, the consensus sequences of the entire polyprotein coding regions of the wild type JFH1 and three chimeric viruses were determined. (monash.edu)
Proteins2
  • Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. (embl.de)
  • At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. (embl.de)
Motifs3
  • In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. (biomedcentral.com)
  • Hence, groups of motifs for co-operating factors will often occur in close proximity to each other in the DNA sequence, and such "composite motifs", or cis -regulatory modules (CRM), can provide a stronger signal than individual motifs. (biomedcentral.com)
  • TF binding motifs may be used either to predict TFBSs on DNA sequences or as reference when annotating/comparing de novo motifs. (genereg.net)
Lengths1
  • In that case one allows for deletions and The distribution of record lengths and the number of entries insertions (presumably originating during evolution), when for each letter are shown in Fig. 1. (lu.se)
Gene expression2
  • Protein synthesis in yeast was found to be highly affected by composition of the Kozak sequence in yeast, with adenine enrichment resulting in higher levels of gene expression. (wikipedia.org)
  • Our results revealed unexpected effects of bldA mutation on gene expression during growth and the transition phase that precedes entry into stationary phase, as well as more wide-ranging effects on secondary metabolism than previously suspected, and led to further exploration of some of the underpinning mechanisms. (biomedcentral.com)
Generates2
  • Once you submit your request, the GeneOptimizer software generates the DNA sequence that best suits your research requirements, based on consideration of all parameters that are relevant for the given host organism plus your individual sequence requirements. (thermofisher.com)
  • The kit generates high-yield, similar-sized libraries that lead to performance improvements in sequence uniformity and overall read depth. (qiagen.com)
Putative2
  • In contrast to c-Myc, the putative Myc antagonist Mnt is maintained at a constant level during cell cycle entry. (silverchair.com)
  • analyzed an expressed sequence tag (EST) database of the model legume M. truncatula and determined and characterized putative gene products or tentative consensus sequences (TCs) specifically expressed in root nodules. (biomedcentral.com)
Transcription3
  • Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis -regulatory modules. (biomedcentral.com)
  • PFMs can be transformed to probabilistic models to construct position weight matrices (PWMs) or position-specific scoring matrices (PSSMs), which then can be used to scan any DNA sequence and predict transcription factors binding sites (TFBSs). (genereg.net)
  • These selections have been used to recover lines that block early postentry stages of infection, either before reverse transcription or before nuclear entry. (biomedcentral.com)
Codon4
  • The sequence was defined as 5'-(gcc)gccRccAUGG-3' (IUPAC nucleobase notation summarized here) where: The underlined nucleotides indicate the translation start codon, coding for Methionine. (wikipedia.org)
  • A suboptimal Kozak sequence can allow for PIC to scan past the first AUG site and start initiation at a downstream AUG codon. (wikipedia.org)
  • The ribosome assembles on the start codon (AUG), located within the Kozak sequence. (wikipedia.org)
  • We have conducted several internal studies, and many customers have reported independently that GeneArt codon and sequence optimization results in higher protein expression without losing protein function. (thermofisher.com)
Ribosomal1
  • The Kozak sequence is not to be confused with the ribosomal binding site (RBS), that being either the 5′ cap of a messenger RNA or an internal ribosome entry site (IRES). (wikipedia.org)
20232
  • Available online: https://encyclopedia.pub/entry/10926 (accessed on 10 December 2023). (encyclopedia.pub)
  • The ADAMTS/Fibrillin Connection" Encyclopedia , https://encyclopedia.pub/entry/10926 (accessed December 10, 2023). (encyclopedia.pub)
Https1
Consists1
  • The ancillary domain, which mediates binding to ECM components and specific protease substrates, consists of a conserved central thrombospondin type 1 sequence repeat motif (TSR), a cysteine-rich domain and a spacer domain. (encyclopedia.pub)
Represents1
  • This entry represents a most populated subfamily of leucine-rich repeats. (embl.de)
Facilitate2
  • The HCV glycoproteins E1 and E2 are present on the surface of virions as a heterodimer that attach virions to host cell receptors and facilitate virus fusion and entry. (monash.edu)
  • Sequence information will facilitate research on vaccine development. (cdc.gov)
Results3
  • The sequence must be written into Analysis Results! (zfmk.de)
  • These results demonstrate that Mnt-Myc antagonism plays a fundamental role in regulating cell cycle entry and proliferation. (silverchair.com)
  • Plasmid transfection was evaluated using X-gal staining.Results: Sequencing of the PCR products revealed the insertion of the desired substitutions in the exact positions. (ac.ir)
Receptors2
  • Recently, claudin-1 and occludin have emerged as additional receptors required for entry. (monash.edu)
  • It seems that "glycosylation consensus" has important role in the receptor and also, other cell surface receptors. (ac.ir)
Protein1
  • Regarded as the optimum sequence for initiating translation in eukaryotes, the sequence is an integral aspect of protein regulation and overall cellular health as well as having implications in human disease. (wikipedia.org)
Next-generation1
  • Although next-generation sequencing (NGS) has become a vital tool, library preparation remains a key bottleneck in the NGS workflow. (qiagen.com)
Expression3
  • This may also be true for autologous expression, since wild type sequences are not necessarily optimized for expression yield but also for degradation, regulation, and other properties. (thermofisher.com)
  • Design your synthetic gene by uploading your sequence, selecting your expression system, and specifying your cloning vector and your sequence details (including open reading frames, untranslated regions, and cloning sites). (thermofisher.com)
  • MWCNT stimulated the expression of a reporter gene under the control of either 5 copies of a NF-kB binding sequence or the mouse TNFa gene promoter that contains multiple copies of the NF-kB binding elements. (cdc.gov)
Variation1
  • Variation within the Kozak sequence alters the "strength" thereof. (wikipedia.org)
Products1
  • The PCR products were sequenced. (ac.ir)
Cell3
  • The c-Myc oncoprotein is strongly induced during the G0 to S-phase transition and is an important regulator of cell cycle entry. (silverchair.com)
  • Mnt overexpression suppressed cell cycle entry and cell proliferation, suggesting that the ratio of Mnt-Max to c-Myc-Max is critical for cell cycle entry. (silverchair.com)
  • Furthermore, simultaneous Cre-Lox mediated deletion of Mnt and c-Myc in mouse embryo fibroblasts rescued the cell cycle entry and proliferative block caused by c-Myc ablation alone. (silverchair.com)
Delivers1
  • It considers all relevant optimization parameters in a single operation and delivers a DNA sequence configured with your specifications, optimized for maximum performance in your system ( Table 1 ). (thermofisher.com)
Journal2
  • Below I describe a couple of subsequent submissions for the EMBO Journal 2011 Cover Contest - a scientific entry and a non-scientific entry. (bcgsc.ca)
  • For the EMBO Journal 2011 Cover Contest , I prepared two entries, one for the scientific category and one for the non-scientific category. (bcgsc.ca)
Found1
  • While the +4 and the −3 positions in the Kozak sequence have the greatest relative importance in the establishing a favorable initiation context a CC or AA motif at −2 and −1 were found to be important in the initiation of translation in tobacco and maize plants. (wikipedia.org)
Complete1
  • Participants reflected that this type of cooperation is what allowed scientists to develop safe and effective COVID-19 vaccines in less than a year, and in the case of Brazil, it allowed the country to be the first in Latin America to complete genetic sequencing of the coronavirus. (as-coa.org)
Mechanisms2
  • The roundtable convened policymakers, renowned medical doctors, and thought leaders with the objective of analyzing the mechanisms needed for rebuilding the consensus on vaccines in Brazil, particularly looking at strategies to generate acceptance and uptake for vaccines, while discussing lessons learned and developing strategies to be adopted by the government going forward. (as-coa.org)
  • Participants suggested that the government should implement innovation-enabling regulations, as well as mechanisms to make the entry of new technologies somewhat more flexible. (as-coa.org)
Analysis1
  • Sequence analysis revealed mutations in core, NS2, NS5A and NS5B. (monash.edu)
Database3
  • The situation is very similar to the one occurring in The database contains 6938 entries on 2652 patients and multisequence alignment when comparing DNA (4-letter although limited in size, it is representative of the noisy and code) or amino acid (20-letter code) strings within incomplete real-world conditions we intend to characterize. (lu.se)
  • The blockchain structure is based on a decentralized network, database immutability, block hashing, smart contracts, and a consensus. (medium.com)
  • This online archive of the CDC Prevention Guidelines Database is being maintained for historical purposes, and has had no new entries since October 1998. (cdc.gov)
Abstract1
  • The non-scientific entry is abstract photo of fiber optics. (bcgsc.ca)
Sites1
Reference1
  • The reference output is like this: References Schneider T.D.and Stephens R.M. Sequence Logos: A New Way to Display Consensus Sequences. (tug.org)
Base1
  • R' indicates that a purine (adenine or guanine) is always observed at this position (with adenine being more frequent according to Kozak) a lower-case letter denotes the most common base at a position where the base can nevertheless vary the sequence in parentheses (gcc) is of uncertain significance. (wikipedia.org)
Block2
  • Simply increasing block sizes for greater transaction throughput requires more powerful hardware to run full nodes and thus, will increase entry barriers, leading to less decentralization of the network. (theblock.co)
  • Each block is protected by a hash function that converts the entries into a sequence of numbers that is extremely difficult to guess. (medium.com)