• MSA refers to the alignment of three or more biological sequences, protein or nucleic acid of similar length. (projectguru.in)
  • Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
  • Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
  • many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
  • A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
  • Major technological advances in affordable nucleic acid sequencing have allowed for an explosion of sequencing data and molecular tools available for researchers in biological sciences. (lu.se)
  • It can align both protein and DNA sequences, and expects inputs to be in fasta format. (arizona.edu)
  • Protein sequence, in FASTA format. (lu.se)
  • Protein sequences: (in FASTA format),e.g. (lu.se)
  • For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. (wikipedia.org)
  • For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. (wikipedia.org)
  • The first and most important step in studying a newly discovered protein sequence is to search protein databases for proteins that are similar or closely-related to the new protein, and then to align the new protein sequence to these proteins. (concordia.ca)
  • It also determines the consensus sequence of the aligned sequences and reveals biological facts about proteins. (projectguru.in)
  • DNA, RNA sequences as well as proteins have been disclosed in patents since the 60s and a few even before that. (questel.com)
  • The zipped file contains multiple sequence alignment of sequences similar to the proteins containing variants in the training and test data. (lu.se)
  • The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. (nyu.edu)
  • Multiple Sequence Alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. (cshl.edu)
  • Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. (wikipedia.org)
  • Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. (wikipedia.org)
  • Insertion/deletion (indel) and substitution of an amino acid are two common events that lead to the evolution of and variations in protein sequences. (concordia.ca)
  • Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. (vu.nl)
  • Recently, members of the Usually Multiple Amino acids Move In and Out Transporter (UMAMIT) family were shown to be essential for facilitating transport of seed-bound glucosinolates from site of synthesis within the reproductive organ to seeds. (frontiersin.org)
  • First, there is a common language to describe DNA/RNA and amino acid sequences, entirely independent from the native language the patent is written in. (questel.com)
  • HCirV-1 shared 70% amino acid identity with the closest known viral sequences. (cdc.gov)
  • Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)
  • Similar kinds of things were done for amino acid sequencing, a very different kind of language. (medscape.com)
  • It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment. (altlinux.org)
  • The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. (bioconductor.org)
  • Details of the algorithms used in Opal are available in the original ISMB paper, which should be cited in the event Opal is used: Wheeler, T.J. and Kececioglu, J.D. Multiple alignment by aligning alignments, Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics 23, i559-i568, 2007. (arizona.edu)
  • Details of this approach are available in the following paper, which should be cited if secondary-structure-based alignment is performed: Kim, E., Wheeler, T.J., and Kececioglu, J.D. Learning models for aligning protein sequence with predicted secondary structure, Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics 5541: 586-605, 2009. (arizona.edu)
  • Thus, the alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics analyses, and has been used in many applications, including sequence annotation, phylogenetic tree estimation, evolutionary analysis, secondary structure prediction and protein database search. (concordia.ca)
  • Computational algorithms are used to produce and analyse the MSAs due to the difficulty and intractability of manually processing the sequences given their biologically-relevant length. (wikipedia.org)
  • In spite of considerable research and efforts that have been recently deployed for improving the performance of multiple sequence alignment (MSA) algorithms, finding a highly accurate alignment between multiple protein sequences still remains a challenging problem. (concordia.ca)
  • This program switches between different alignment algorithms and between sequences and profiles, so I wanted to create a library that aligns any collection of objects with various algorithms using the same syntax. (github.com)
  • The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade. (bioconductor.org)
  • They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. (plos.org)
  • Starting in the 90s, and the human genome project, genomic and mRNA sequences started to become more common in patents. (questel.com)
  • We recommend taking a plurality consensus sequence for each gene segment, genome, and/or lineage/subtype. (cdc.gov)
  • 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)
  • Transposable elements refer to DNA sequences capable of moving from one part of the genome to another. (lu.se)
  • In the previous article , similar gene sequences of an established mercuric ion reductase or merA gene were identified. (projectguru.in)
  • This article further explores the merA gene sequence analysed in the previous article . (projectguru.in)
  • Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies. (leibniz-lib.de)
  • Thymidine kinase gene amplicon sequences (339 bp) from 21 lynx were all identical to those of poxviruses to new regions through relocation of their from cowpox virus isolated from a person in Norway and natural host species is possible ( 10 ). (cdc.gov)
  • Phylogenetic studies showed that the HCoV-HKU1 nucleoprotein gene was relatively conserved compared to NCBI reference sequences, while the 1ab gene of HCoV-NL63 showed more variation. (hindawi.com)
  • The full HA and NA genes of 16 H1N1-positive samples obtained in our study and 21 published HA sequences and 20 published NA sequences from Jordanian viruses that were available on online gene databases were analysed. (who.int)
  • Next, the isolates were differentiated by sequencing a specific region of the gene encoding the enzyme glucosyltransferase B ( gtfB ). (bvsalud.org)
  • Conclusions: The partial sequencing of the gtfB gene can be a useful tool for elucidating the colonization patterns of S. mutans . (bvsalud.org)
  • In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)
  • All 10x Genomic services include a final report containing a Cell Ranger web summary file for quality control (QC) of the sequencing outcome, as well as FASTQ, BAM, gene count matrix containing all single cells or nuclei passing QC, basic visualization and clustering. (lu.se)
  • Usage of reporter genes need to be specified in iLab before project start and the exact sequence information and gene co-ordinates need to be submitted to be included during sequencing read alignment. (lu.se)
  • From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
  • This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. (vu.nl)
  • Areas that will be covered include: sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
  • This week€™s addition to the virology toolbox was written by Chris Upton The Jalview package: a multiple alignment editor. (virology.ws)
  • Sequence divergence within oligonucleotide-binding sites creates primer-template duplex instability and lowers T m . (nature.com)
  • Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. (providence.org)
  • We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family. (providence.org)
  • It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions. (leibniz-lib.de)
  • We propose an alternative method which can identify random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. (leibniz-lib.de)
  • The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. (leibniz-lib.de)
  • In consequence, consensus profiles identify dominating patterns of non-random similarity or randomness within sections of multiple sequence alignments. (leibniz-lib.de)
  • COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. (nih.gov)
  • COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. (nih.gov)
  • See Edgar RC, Nucleic Acids Res 16:380-5, 2004, PMID: 14729922 for k-mer counting-based sequence similarity. (nih.gov)
  • Number of letters in a word (k-mer) for k-mer count-based sequence similarity computation. (nih.gov)
  • This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)
  • Constructing alignments is necessary for phylogenetic reconstruction, but also for many other types of evolutionary analyses. (utexas.edu)
  • In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. (illinois.edu)
  • While BESTFIT's randomize is rather crude I should recommend W.Pearson's RDF2 which also permits to suffle *windows* of the sequence, thus leaving the sequence more intact than the pure monte carlo would permit. (bio.net)
  • In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. (wikipedia.org)
  • Query sequences to be aligned should be pasted in the text area. (nih.gov)
  • Use RPS-BLAST to find conserved domains in query sequences to guide alignment. (nih.gov)
  • In this article, the protein sequence of merA enzyme is studied with respect to its closely related sequences found in NCBI database, through Multiple Sequence Alignment (MSA) . (projectguru.in)
  • The quality of the alignment can then be represented by the sum-of-pairs (SP) or column (CS) scores, which measure the agreement between a reference and corresponding query alignment. (vu.nl)
  • Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)
  • In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. (wikipedia.org)
  • In response to this challenge, we introduce PASTA, a scalable and accurate algorithm that can align datasets with up to a million sequences. (utexas.edu)
  • The objectives of this thesis are to develop a novel scheme to predict indel flanking regions (IndelFRs) in a protein sequence and to develop an efficient algorithm for the alignment of multiple protein sequences incorporating the information on the predicted IndelFRs. (concordia.ca)
  • In the second part of the thesis, a novel and efficient algorithm incorporating the information on the predicted IndelFRs for the alignment of multiple protein sequences is proposed. (concordia.ca)
  • The performance of the proposed alignment algorithm, named as MSAIndelFR algorithm, is evaluated in terms of the so called metrics, sum-of-pairs (SP) and total columns (TC). (concordia.ca)
  • In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. (nyu.edu)
  • Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. (nyu.edu)
  • Here, we implement a smooth and differentiable version of the Smith-Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. (cshl.edu)
  • When little is known about the features of input sequences, the new default is safer, because less likely to make serious errors. (cbrc.jp)
  • Ranges of input sequences that match to the same conserved domain will be aligned to each other in the final multiple alignment. (nih.gov)
  • E-value threshold for accepting BLAST-P hits in pair wise local alignment of input sequences. (nih.gov)
  • Pair wise locally aligned ranges of input sequences will be aligned to one another in the multiple alignment. (nih.gov)
  • Identify conserved columns after the first iteration of progressive alignment and re-align input sequences using this information. (nih.gov)
  • We recommend using this option for aligning BLAST results and whenever a subset of input sequences that share conserved domains is expected. (nih.gov)
  • then only the maximum hit for all reference sequences will be grouped into primary data. (cdc.gov)
  • During my Ph.D. studies, my focus has been analyzing sequencing data in relation to transposable elements. (lu.se)
  • My focus has been on the data analysis side of things, employing different computational methods to deal with mapping ambiguity and adapting new technologies such as single-cell RNA sequencing to better understand three families of transposable elements. (lu.se)
  • ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)
  • The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. (wikipedia.org)
  • Gap opening penalty and gap extension penalty for gaps inside of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)
  • Gap opening penalty and gap extension penalty for gaps at ends of a sequence used in pairwise global alignment in the progressive alignment stage. (nih.gov)
  • In-cluster sequences will be aligned using combined local and global alignment. (nih.gov)
  • Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. (wikipedia.org)
  • Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. (wikipedia.org)
  • There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. (wikipedia.org)
  • The amount of biological sequence data is increasing rapidly, a promising development that would transform biology if we can develop methods that can analyze large-scale data efficiently and accurately. (utexas.edu)
  • History: Alignlib contains a collection of methods for classical biological sequence alignment. (github.com)
  • Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. (vu.nl)
  • Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. (vu.nl)
  • However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. (vu.nl)
  • We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. (vu.nl)
  • Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. (illinois.edu)
  • This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. (cshl.edu)
  • Accuracy of multiple sequence alignment methods in the reconstruction " by Robert Hubley, Travis J Wheeler et al. (providence.org)
  • Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. (providence.org)
  • This tutorial will serve as a consolidation space for all existing help on Coloring methods in Multiple Sequence Alignment View. (nih.gov)
  • Alignment Scoring Methods menu will be displayed. (nih.gov)
  • Methods: S. mutans samples were isolated from the saliva of 30 children with varying histories of dental caries, and they were characterized according to morphological and biochemical markers and the sequences of their 16S-23S intergenic spacer region. (bvsalud.org)
  • Determination of the transmembrane topology of a protein starts with a model of the protein based on sequence information and theoretical methods. (lu.se)
  • In this project, we use principles from multidimensional solid-state NMR spectroscopy to design new MRI pulse sequences and data processing methods for investigating cell density, shape, alignment, heterogeneity, and membrane permeability. (lu.se)
  • Why do recent versions generate LONG alignments? (cbrc.jp)
  • Returns only the alignments used to generate the HMM profile. (mathworks.com)
  • Generate a phylogenetic tree from aligned sequences. (mathworks.cn)
  • You can also generate a phylogenetic tree from aligned sequences from within the app. (mathworks.cn)
  • To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. (providence.org)
  • MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. (wikipedia.org)
  • As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. (cshl.edu)
  • Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. (illinois.edu)
  • One challenges is aligning large number of sequences so that evolutionarily related positions in all sequences are put in the same column. (utexas.edu)
  • This is facilitated by directing primer and probe design to evolutionarily conserved regions identified through multiple sequence alignments that portray geographical and temporal genomic variability. (nature.com)
  • Then computationally intensive tasks of identifying conserved domains and consistent set of constraints can be avoided for many sequences. (nih.gov)
  • We found no other viral or bacterial sequences. (cdc.gov)
  • Alternatively, you can click Sequence Alignment on the Apps tab to open the app, and view the alignment data. (mathworks.cn)
  • Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R? (stackexchange.com)
  • The standard output also includes a .cloupe file for exploring your samples with the 10x Loupe browser for each sample individually as well as for multiple samples as aggregated data. (lu.se)
  • Other classes ending in -or perform other tasks like building trees (Treetor) or weight sequences (Weightor) Alignata: things that have been aligned. (github.com)
  • For each cluster, the MSA is calculated using Clustal Omega and displayed in the 1D-3D Group Alignment Viewer using specific color schemes. (rcsb.org)
  • Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)
  • To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
  • Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. (providence.org)
  • RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. (bvsalud.org)
  • This distance overestimates exponentially scaled percentage of different residues in aligned sequences (see graphs in the above paper for details). (nih.gov)
  • Through the study undertaken in this thesis it is shown that a reliable detection of indels and their flanking regions can be achieved by using the proposed IndelFR predictors, and a substantial improvement in the protein alignment accuracy can be achieved by using the proposed variable gap penalty function. (concordia.ca)
  • A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (wikipedia.org)
  • We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. (illinois.edu)
  • Additionally, randomly similar sequences or ambiguously aligned sequence sections can negatively interfere with the estimation of substitution model parameters. (leibniz-lib.de)
  • Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. (nyu.edu)
  • Maximum allowed distance between two sequences in a cluster. (nih.gov)
  • which should be used to create and submit scripts for Hisat alignment to the cluster. (lu.se)
  • qPCR probe design is more averse to similar modifications because increasing probe T m through nucleotide degeneracy or sequence lengthening may lead to high T m variations that reduce specific target discrimination. (nature.com)
  • The SP score and the SPdist score yield very similar outcomes when the reference and query alignments are close. (vu.nl)
  • Third, unless your sequence is very short, you will always want to find sequences similar to yours, not just identical. (questel.com)
  • Reduce computation time by using clusters of similar sequences. (nih.gov)
  • The idea behind using clusters is that constraints do not contribute information for alignment of very similar sequences. (nih.gov)
  • Clusters of similar sequences are found using alignment-free k-mer counting-based method. (nih.gov)
  • Smaller words will make sequences more similar than larger words. (nih.gov)
  • tag and are similar to options alread present for the legacy tophat alignment. (lu.se)
  • We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. (nature.com)
  • Specimens were collected from 9 provinces during 2 seasonal activities in 2001-2002, identified morphologically and subjected to PCR assay and direct sequencing. (who.int)
  • As new protein sequences are discovered on an everyday basis and protein databases continue to grow exponentially with time, analysis of protein families, understanding their evolutionary trends and detection of remote homologues have become extremely important. (concordia.ca)
  • Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
  • When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
  • Agnostic metagenomic analysis of clinical samples based on next-generation sequencing (NGS) combined with specifically designed PCRs constitute promising tools for diagnosing infection with unforeseen or novel microorganisms ( 8 ). (cdc.gov)
  • HA and NA sequences each in the analysis. (who.int)
  • A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. (wikipedia.org)
  • An optimal hidden path emitting Text in HMM(Alignment,θ,σ). (rosalind.info)
  • For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. (wikipedia.org)
  • To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. (cshl.edu)
  • A string Text, a multiple alignment Alignment, a threshold θ, and a pseudocount σ. (rosalind.info)
  • RCSB.org clusters protein entities (PDB experimental structures and CSMs) by sequence identity threshold and UniProt accession. (rcsb.org)
  • This threshold prvents COBALT from forming clusters o unrelated sequences. (nih.gov)
  • Obviously, pharmaceutical industry, biotech, agrochemical and seed companies produce the bulk of sequence patents. (questel.com)
  • After ruling out common etiologies, we used metagenomic next-generation sequencing to analyze a liver biopsy sample and identified an unknown species of circovirus, tentatively named human circovirus 1 (HCirV-1). (cdc.gov)
  • Based on plastid encoded DNA sequences from psb A and rbc L markers, these species belong in the subfamily Chamberlainoideae. (degruyter.com)
  • The DNA sequences, supported by the morpho-anatomical character of tetrasporangial conceptacle roof development, placed all three species in the genus Chamberlainium and not Pneophyllum , the only other genus in Chamberlainoideae. (degruyter.com)
  • By sequencing the 16S-23S intergenic region, it was found that all of the isolates belonged to the species S. mutans . (bvsalud.org)
  • Alignments by the new default are generally longer than those by the old default. (cbrc.jp)
  • We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. (illinois.edu)