• Therefore comparative genomic analysis of T . equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T . equi relative to sequenced apicomplexan parasites. (biomedcentral.com)
  • Comparative genomic analysis of T . equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp . (biomedcentral.com)
  • They develop methods that can learn conserved structures, functions, features, and motifs from known protein and DNA sequences and use them to predict the function and structures of novel genes and proteins from the genomic efforts. (nationalacademies.org)
  • MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. (biomedcentral.com)
  • MicroRNAs (miRNA) are ~22nt non-coding regulatory genes that target other RNA molecules via sequence-specific hybridization, which results either in translation inhibition (an imperfect target miRNA sequence match) or in cleavage and degradation of the targeted RNA (a perfect target miRNA sequence match) [ 1 ]. (biomedcentral.com)
  • The most rigorous and general method for creating a comparative genomic mapping of functionally-equivalent genes across species is through the use of phylogenetics to infer evolutionary relationships. (biorxiv.org)
  • For any given set of species, gene families are created by first identifying all the genes in all species and then clustering them based on their sequence similarities. (biorxiv.org)
  • have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
  • Coding region inhomogeneity, caused by differences in sequence composition between "native" and horizontally transferred genes or between genes expressed at different levels, contributes to the false negative error rate. (aaai.org)
  • We have documented such unnoticed genes in GenBank sequences for several species. (aaai.org)
  • Some of protein products of these genes have been characterized by similarity search methods. (aaai.org)
  • For others, which we call "pioneer genes", no significant similarity has been found at a protein sequence level although the confidence of GeneMark prediction is high. (aaai.org)
  • Prior to the "genomic era," when the acquisition of DNA sequence involved significant labor and expense, the sequencing of genes was strongly linked to the experimental characterization of their products. (plos.org)
  • Full genome sequencing can reveal the approximately 13,500-letter sequence of all the genes of the influenza virus' genome. (cdc.gov)
  • The sequences deposited into these databases allow CDC and other researchers to compare the genes of currently circulating influenza viruses with the genes of older influenza viruses and those used in vaccines. (cdc.gov)
  • Detecting Staphylococcus aureus Virulence and Resistance Genes - a Comparison of Whole Genome Sequencing and DNA Microarray Technology. (cdc.gov)
  • However, Fleischman and colleagues did not detect mutations in the coding sequence of HOX genes known to affect radial development. (medscape.com)
  • Modern high-throughput metagenomics is producing hundreds of thousands of metagenome-assembled genomes (MAGs), which is overwhelming traditional sequence-similarity search methods. (nature.com)
  • Students will be introduced to biological sequence data (DNA and protein sequences, whole genomes, learn to access major sequence databases and use a variety of web-based services. (uit.no)
  • Bob, you can sequence genomes and understand gene function without knowing a thing about their past and from whence they developed. (uncommondescent.com)
  • This paper is supposed to bridge the gap between practical experience in using GeneMark for a rapidly widening repertoire of genomes, and the available publications that determine and compare the gene prediction accuracy of the GeneMark method for different genomes. (aaai.org)
  • Another practical question is related to genomic sequence inhomogeneity at interspecies level: if GeneMark has not been trained for a particular species, is it possible to apply models derived for phylogenetically close genomes? (aaai.org)
  • Now that DNA sequencing has become orders of magnitude faster and less expensive, focus has shifted to sequencing entire genomes. (plos.org)
  • Sequencing Ebola and Marburg viruses genomes using microarrays. (cdc.gov)
  • Fungal rRNA sequencing of indoor and occupational air samples. (cdc.gov)
  • In this pilot study, rRNA sequencing was utilized to examine the diversity of fungal species present in indoor and occupational environments. (cdc.gov)
  • For molecular analyses, DNA was collected and rRNA sequences were amplified with universal fungal primers. (cdc.gov)
  • We used 3 different approaches: biochemical testing, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and 16S ribosomal RNA (rRNA) gene sequencing. (medscape.com)
  • A concordant identification of P. multocida was observed using biochemical testing, mass spectrometry, and 16S rRNA gene sequencing. (medscape.com)
  • Only 16S rRNA sequencing was able to determine the subspecies of P. multocida and to determine the genetic relatedness of the 2 isolates. (medscape.com)
  • A very successful means of inferring the function of a previously unannotated protein is via sequence similarity with one or more proteins whose functions are already known. (columbia.edu)
  • Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations. (beds.ac.uk)
  • For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. (lu.se)
  • We identify several categories of protein functions where global shape similarity is significantly more likely than expected by random chance, when comparing proteins with little similarity on the fold level. (lu.se)
  • In particular, we find that global surface shape similarity is particular common among DNA binding proteins. (lu.se)
  • For instance, to date a majority of those pioneer gene predictions made for E. coil now show strong similarity to more recently characterized proteins that have been added to protein sequence database. (aaai.org)
  • Maximizing our understanding of function over the universe of proteins in toto requires not only robust computational methods of inference but also a judicious allocation of experimental resources, focusing on proteins whose experimental characterization will maximize the number and accuracy of follow-on predictions. (plos.org)
  • The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family. (plos.org)
  • This set of known sequence-function relationships will ultimately serve as the basis for making predictions for similar proteins whose functions have not been experimentally determined and can be used to train other types of prediction-generating algorithms. (plos.org)
  • Proteins are made of sequences of amino acids. (cdc.gov)
  • This measure comes along with the caveat of possibly high sequence similarity does not necessarily imply homology. (beds.ac.uk)
  • Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. (uni-hamburg.de)
  • Based on the results of phylogenetic similarity of 16SrDNA gene sequences, strain DB17 was identified to be Pseudomonas putida. (omicsonline.org)
  • CDC contributes gene sequences to public databases, such as GenBank and the Global Initiative on Sharing Avian Influenza Data (GISAID) , for use by researchers and public health scientists. (cdc.gov)
  • Currently, one of the most powerful such homology detection methods is the SVM-Fisher method of Jaakkola, Diekhans and Haussler (ISMB 2000). (columbia.edu)
  • Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. (beds.ac.uk)
  • Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. (beds.ac.uk)
  • The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. (beds.ac.uk)
  • The sequence homology concept [ 1 - 3 ] is collectively founded upon the inductive reasoning that a homologous protein group (as an antecedent) shares a high level of sequence similarity (as a consequent) [ 4 - 8 ]. (beds.ac.uk)
  • Despite the simplicity and elegance of the sequence homology concept, homology itself is not readily computable. (beds.ac.uk)
  • Worse, as we delve deeper into sequence search space, high sequence divergence among the distant homologs will inevitably corrupt the homology signal. (beds.ac.uk)
  • Multiple clonal bands in HT had sequence similarity (homology) of 62-100% with the clonal band in the lymphoma from the same patient. (bmj.com)
  • At least one clonal band in HT had more than 96% similarity (homology) with the clonal band of lymphoma in all three cases. (bmj.com)
  • The megaBLAST nucleotide-nucleotide search, optimized for very similar sequences (in the same or in closely related species), first looks for an exact match of 28 bases, and then attempts to extend that initial match into a full alignment ( 3 , 4 ). (nih.gov)
  • The BLASTN nucleotide-nucleotide search looks for more distant sequences. (nih.gov)
  • Amplified HIV DNA was molecularly cloned, and nucleotide sequences of multiple clones were determined. (cdc.gov)
  • Amplicons were cloned, sequenced, and used in BLAST searches against the NCBI nucleotide database to determine the closest fungal relative based on sequence similarity. (cdc.gov)
  • PON-mt-tRNA is a multifactorial-probability method to predict the pathogenicity of single nucleotide substitutions in human mitochondrial tRNAs. (lu.se)
  • In sociology, sequence techniques are most commonly employed in studies of patterns of life-course development, cycles, and life histories. (wikipedia.org)
  • Some complex machine learning methods such as support vector machines, neural networks, and deep learning are black box that means it is difficult for them to interpret fraud patterns, while interpretability is the key to designing fraud prevention mechanisms [ 9 ]. (hindawi.com)
  • From sequence similarities and expression patterns, laccase sensu stricto subfamily 1 can be divided into two subgroups. (springeropen.com)
  • Multiple representations of sequences include simple motif consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches, and computer simulations. (nationalacademies.org)
  • A novel method and a framework called Memory-Based Forecasting are proposed to forecast complex and time-varying natural patterns with the goal of supporting experts' decision making. (aaai.org)
  • Statistical experiments using weather radar images verify the effectiveness of our method and framework especially for drastically changing patterns. (aaai.org)
  • By applying HLFs analysis, sequence similarity and live-indexing clustering methods, WhoLoDance will also make it possible to develop and train multi-modal feature extraction algorithms and related applications (search, real-time feedback, classification, automated annotation, etc.) leading to automatic identification and comparison of dance patterns and styles. (coventry.ac.uk)
  • In bacterial isolates of prisoners and ex-prisoners from the general population, there were 2 strains, which had identical banding patterns, while there were clear similarities between several isolates. (who.int)
  • Sequence analysis methods were first imported into the social sciences from the information and biological sciences (see Sequence alignment) by the University of Chicago sociologist Andrew Abbott in the 1980s, and they have since developed in ways that are unique to the social sciences. (wikipedia.org)
  • Hence, the only recourse to maintain on the correct search path is to piggyback on the similarity between the structural pieces of the alignment to ensure reasonable fold similarity and, hence, the implied biological function. (beds.ac.uk)
  • There are many ways of performing a sequence similarity search, but probably the most popular method is the "Basic Local Alignment Search Tool" ( BLAST ) ( 1 , 2 ). (nih.gov)
  • If instead BLAST started out by attempting to align two sequences over their entire lengths (known as a global alignment), fewer similarities would be detected, especially with respect to domains and motifs. (nih.gov)
  • 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)
  • 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)
  • Use RPS-BLAST to find conserved domains in query sequences to guide alignment. (nih.gov)
  • The sequence matches to conserved domains will be converted into pair wise alignment constraints. (nih.gov)
  • 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)
  • 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)
  • In-cluster sequences will be aligned using combined local and global alignment. (nih.gov)
  • Note that you can also run the alignment method ASCONA locally. (uni-hamburg.de)
  • MultiDisp is a multiple sequence alignment visualization tool that can be used to show sequence properties in several ways. (lu.se)
  • Although the viral sequences from the dentist and the patient could be distinguished from each other, they were closer than what has been observed for pair-wise comparisons of sequences taken from the other North American isolates studied (3). (cdc.gov)
  • To identify the gram-negative rods grown from blood cultures and a right-knee fluid aspirate from an 80-year-old caucasian man who had undergone a total right knee arthroplastic procedure 6 years ago, and to assess the genetic similarity between the 2 isolates. (medscape.com)
  • In a previous work we presented the ∑-gram distance that computes the similarity between two sequences. (coventry.ac.uk)
  • Despite some connections, the aims and methods of SA in social sciences strongly differ from those of sequence analysis in bioinformatics. (wikipedia.org)
  • The BLAST algorithm is tuned to find these domains or shorter stretches of sequence similarity. (nih.gov)
  • BLASTP performs protein-protein sequence comparison, and its algorithm is the basis of many other types of BLAST searches such as BLASTX and TBLASTN . (nih.gov)
  • PSI-BLAST can then search a database of protein sequences with this PSSM. (nih.gov)
  • DELTA- BLAST produces a PSSM with a fast RPSBLAST search of the query , followed by searching this PSSM against a database of protein sequences ( 5 ). (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)
  • Expressed sequence tag (EST) analysis and developmental polymerase chain reaction (PCR) studies demonstrated that Ov-phy-1 was expressed in L3 and adult parasites. (embl.de)
  • HIV sequences encoding the variable regions (V3, V4, and V5) and a constant region (C3) of the major external glycoprotein gp120 were selectively amplified using the polymerase chain reaction (PCR) (1). (cdc.gov)
  • The objective of the study was to develop a rapid method to detect Mycobacterium tuberculosis from clinical samples and the applicability of DNA amplification techniques to a developing country like Sri Lanka. (who.int)
  • In this study, the potential use of PCR was investigated using the primers Pt8-Pt9 based on the insertion sequence IS 6110 of the Mycobacterium tuberculosis complex (Kolk etal, 1992). (who.int)
  • In this study 465 clinical samples were tested using PCR and the results obtained indicates that this approach offers may advantages over conventional methods and could be used to detect Mycobacterium tuberculosis in clinical samples. (who.int)
  • In conclution, DNA amplification is a rapid, reliable and accurate method with a high degree of sensitivity and specificity for the detection of Mycobacterium tuberculosis DNA sequences and it can replace the conventional culture method in the diagnosis of extra pulmonary tuberculosis and tuberculosis meningitis except in the situation when antibiotic sensitivity results are required. (who.int)
  • A search allows scientists to infer the function of a sequence from similar sequences. (nih.gov)
  • Reduce computation time by using clusters of similar sequences. (nih.gov)
  • Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. (beds.ac.uk)
  • 2015. Quantifying similarity in animal vocal sequences: which metric performs best? (nimbios.org)
  • In a typical year, CDC performs whole genome sequencing on about 7,000 influenza viruses from original clinical samples collected through virologic surveillance. (cdc.gov)
  • PON-Diso a machine learning based prediction method to predict changes in disorder regions contained in a protein, caused by amino acid substitutions. (lu.se)
  • PON-Sol is a two-step machine learning-based method to predict the impact of amino acid substitutions on protein solubility. (lu.se)
  • The group uses statistical methods and machine learning to discover first principles of molecular and structural biology from known examples. (nationalacademies.org)
  • Algorithms for estimating similarity between two macromolecular sequences are of profound importance for molecular biology. (iospress.com)
  • One thing that is often done in molecular biology is to ask what a gene does, or what a sequence is involved in. (uncommondescent.com)
  • 2003 ). In 2017, the first chromosome-scale reference genome sequence of quinoa was published, and it has provided the much-needed resource for plant biologists to design molecular breeding and crop improvement programs for quinoa (Jarvis et al. (springer.com)
  • The genome sequence of quinoa serves as an entry point for deciphering the complex molecular pathways that contribute to floral evocation. (springer.com)
  • In the 1990s, however, newer molecular techniques to amplify, sequence, and express the genome of NLV strains allowed researchers to genetically and antigenically characterize NLV strains. (medscape.com)
  • As such, statistically significant yet spurious alignments (attributed by the remnant segments) can pass off as homologous sequences once they escape the designated statistical threshold. (beds.ac.uk)
  • This option can be unchecked for aligning of sequences that are not expected to share conserved domains and are expected to have very short pair wise local alignments. (nih.gov)
  • We present a computational method, skani, that efficiently compares MAGs on a terabyte scale while being robust to the inherent noise in MAGs, enabling larger and more accurate analyses. (nature.com)
  • Compare results from different analyses and from an analytical point of view explain differences and similarities. (lu.se)
  • Examination of direct smears for acid fast bacilli is the widely used method for the detection of mycobacteria, but lacks the desired specificity and relatively large number of bacteria is needed for detection. (who.int)
  • Manual and automated mass spectrometry acquisition of intact protein and peptide mass determination and determination of peptide sequence information. (lu.se)
  • Basic data handling of mass spectrometry data for protein identification, assessment of PTMs and determination of amino acid sequences. (lu.se)
  • In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility to biomedical data is largely unexplored. (mpi-cbg.de)
  • Out of 20 positive samples, 13 (65%) gave satisfactory sequencing results. (lww.com)
  • During the course, the students will learn to retrieve, analyze, compare and visualize genetic sequences. (uit.no)
  • While the methods are similar, there are slight differences in the approaches to RNA and DNA structure prediction. (wikipedia.org)
  • Yes, Dave, the differences are the same, i.e. the observed sequences are the same. (uncommondescent.com)
  • The differences or similarities you discover by these empirical methods are the same no matter how they hypothetically came to exist. (uncommondescent.com)
  • Flash entropy speeds up mass spectral similarity searches 10,000-fold, including for open search, hybrid search and neutral loss search. (nature.com)
  • Implicitly, this refers to a high level of similarity among comparable structural elements across the sequences so that a common structural fold among these homologs is maintained which, in turn, governs the general biological function of this homologous protein family. (beds.ac.uk)
  • Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)
  • In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)
  • The method, SVM-pairwise, uses a pairwise sequence similarity algorithm such as Smith-Waterman in place of the HMM in the SVM-Fisher method. (columbia.edu)
  • The predominant intestinal microbial community consisted of 130 species or phylotypes according to the sequence data in this study. (nih.gov)
  • This method combines a generative, profile hidden Markov model (HMM) with a discriminative classification algorithm known as a support vector machine (SVM). (columbia.edu)
  • In this paper we use this pre-initialization method on the artificial bee colony algorithm to calculate the parameters of the ∑-gram distance. (coventry.ac.uk)
  • The algorithm used to minimize this criterion is a combinatorial optimization method called simulated annealing. (bio.net)
  • ODS: Ordering DNA Sequences, a physical mapping algorithm based on simulated annealing. (bio.net)
  • In social sciences, sequence analysis (SA) is concerned with the analysis of sets of categorical sequences that typically describe longitudinal data. (wikipedia.org)
  • SA is a longitudinal analysis approach that is holistic in the sense that it considers each sequence as a whole. (wikipedia.org)
  • Social network analysts (see Social network analysis) have begun to turn to sequence methods and concepts to understand how social contacts and activities are enacted in real time, and to model and depict how whole networks evolve. (wikipedia.org)
  • Many of the methodological developments in sequence analysis came on the heels of a special section devoted to the topic in a 2000 issue of Sociological Methods & Research, which hosted a debate over the use of the optimal matching (OM) edit distance for comparing sequences. (wikipedia.org)
  • In 2006, David Stark and Balazs Vedres proposed the term "social sequence analysis" to distinguish the approach from bioinformatic sequence analysis. (wikipedia.org)
  • Sociological Methods & Research organized a special issue on sequence analysis in 2010, leading to what Aisenbrey and Fasang referred to as the "second wave of sequence analysis", which mainly extended optimal matching and introduced other techniques to compare sequences. (wikipedia.org)
  • Alongside sequence comparison, recent advances in SA concerned among others the visualization of sets of sequence data, the measure and analysis of the discrepancy of sequences, the identification of representative sequences, and the development of summary indicators of individual sequences. (wikipedia.org)
  • Raab and Struffolino have conceived more recent advances as the third wave of sequence analysis. (wikipedia.org)
  • This wave is largely characterized by the effort of bringing together the stochastic and the algorithmic modeling culture by jointly applying SA with more established methods such as analysis of variance, event history analysis, Markovian modeling, social network analysis, or causal analysis and statistical modeling in general. (wikipedia.org)
  • The human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16S rDNA libraries and a culture-based method. (nih.gov)
  • The formal analysis method is an efficient knowledge representation and discovery tool, such as formal concept analysis (FCA) [ 12 ]. (hindawi.com)
  • Sequence comparison and transcription analysis has been carried out in several basidiomycetous fungi as well, such as Coprinopsis cinerea (Kilaru et al. (springeropen.com)
  • The aim of this workshop is to bridge the gap between mathematical and biological researchers with an interest in the quantitative analysis of animal vocal sequences. (nimbios.org)
  • The intention was that each group would generate a draft section of a manuscript that would provide a comprehensive review of the analysis of animal acoustic sequences. (nimbios.org)
  • Methods of correlation analysis allow for the identification of pairs of residue positions, whose occupancy is mutually dependent due to constraints imposed by protein structure or function. (uni-regensburg.de)
  • The analysis of a large in silico testbed demonstrated that specificity and precision were higher for H2rs than for H2r and two other methods of correlation analysis. (uni-regensburg.de)
  • Finally, we describe deep-learning methods well-suited for 3D analysis of nuclei and classify them according to their level of usability for biologists. (brookes.ac.uk)
  • USING THE SOFTWARE WITHOUT THE PROGRAMS: The programs also have been incorporated into a DNA sequence analysis package (Arnold et al. (bio.net)
  • This multifaceted analysis showed a similarity between the sequences from the patient and the dentist that was comparable to what has been observed for cases that have been epidemiologically linked (Los Alamos National Laboratory, unpublished data). (cdc.gov)
  • however, the etiological agents remain uncharacterized due to the limitations of traditional sampling and analysis methods. (cdc.gov)
  • CONCLUSIONS: Compared to traditional methods of analysis, our data demonstrate a much wider diversity of fungi that may possibly contribute to personal exposure and adverse health effects in home and occupational environments. (cdc.gov)
  • The visualization schemes include graphs for coloured and property charts, identity, similarity and divergence plots as well as visualizations based on physicochemical properties. (lu.se)
  • Randomly selected clones were partially sequenced. (nih.gov)
  • On the basis of sequence similarities, the clones and colonies were classified into several clusters corresponding to the major phylum of the domain Bacteria. (nih.gov)
  • About 75% of the remaining clones were novel "phylotypes" (at least 98% similarity of clone sequence). (nih.gov)
  • Genetics, in press ODS is a program that orders DNA sequences based on similarity of their binary profiles assigned to clones in a library by one of several experimental approaches. (bio.net)
  • CDC and other public health laboratories around the world have been sequencing the gene segments of influenza viruses since the 1980s. (cdc.gov)
  • Methods: Primary breast tumor-derived CAFs were transduced to express human telomerase reverse transcriptase (hTERT) and sorted into CD105 low and CD105 high populations using fluorescence-activated cell sorting (FACS). (lu.se)
  • The two populations were tested for differentiation similarities to iCAF and myCAF states through transcriptome-wide RNA-Sequencing (RNA-Seq) including comparison to an available iCAF-myCAF cell state atlas. (lu.se)
  • In turn, fold conservation implies the conservation of a sequence pattern of hydrophilic/hydrophobic and size-restricted residues within the protein family. (beds.ac.uk)
  • This distance overestimates exponentially scaled percentage of different residues in aligned sequences (see graphs in the above paper for details). (nih.gov)
  • [6] For longer molecules, the number of possible secondary structures is huge: a sequence of 100 nucleotides has more than 10 25 possible secondary structures. (wikipedia.org)
  • Genome sequencing is a process that determines the order, or sequence, of the nucleotides (i.e. (cdc.gov)
  • Genome sequencing reveals the sequence of the nucleotides in a gene, like alphabet letters in words. (cdc.gov)
  • Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
  • For experimental methods, see Nucleic acid structure determination . (wikipedia.org)
  • The structure prediction methods can follow a completely theoretical approach, or a hybrid one incorporating experimental data. (wikipedia.org)
  • Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. (plos.org)
  • Sequencing at that time directly resulted from the need to understand an experimentally determined phenotype or biochemical activity. (plos.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)
  • Moreover, the traditional methods for functional gene discovery are insufficient to meet the modern-day research demands due to the high error rates and low efficiencies. (researchsquare.com)
  • Consequently, such approaches do not consider the similarity of residue pairs, which may degrade the algorithm's performance. (uni-regensburg.de)
  • So for matching multiple files, we should set the first sequence repeatedly. (tutorialspoint.com)
  • These methods find th e substrings of maximal similarity, as defined by the so-called similarity matrix, for a pair of two molecules. (iospress.com)
  • Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. (beds.ac.uk)
  • Regrettably, current implementation of sequence search algorithms do not consciously differentiate between the 3D-structural (i.e., fold-critical) sequence segments and the non-globular (i.e., remnant) segments. (beds.ac.uk)
  • In a benchmark study of structures with the same fold, we show that ZEAL outperforms two other methods for shape-based superposition. (lu.se)
  • 1986), and can be accessed directly on the Biological Sequence/Structure Computational Facility (BS/SCF). (bio.net)
  • TO: Those Interested FROM: Jonathan Arnold, ARNOLD at BSCF.UGA.EDU SUBJECT: ODS DISTRIBUTION INFORMATION ON Ordering DNA Sequences (ODS) ver 1.0 (c) 1990 The Univ of GA & A. Jamie Cuticchia PROGRAM DESCRIPTION: Programs are now available to assist in the in vitro reconstruction of chromosomes or chromosome fragments ('contig mapping') from a clonal library. (bio.net)
  • For the DNA extraction and purification from the clinical samples two methods, the standard phenol extraction procedure desctibed by Sambrook etal (1982) and the guanidinium thiocyanate method described by Boom et al(1990) were used. (who.int)
  • This lack of increase contrasts with previous reports as does the mRNA length: this is 50% larger as confirmed by sequencing the 3' end. (embl.de)
  • Its closest surrogate is the sequence similarity measure. (beds.ac.uk)
  • In the nearest neighbor model the free energy change for each motif depends on the sequence of the motif and of its closest base-pairs. (wikipedia.org)
  • Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
  • Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots . (wikipedia.org)
  • Most popular methods for predicting RNA and DNA's secondary structure involve dynamic programming . (wikipedia.org)
  • This threshold prvents COBALT from forming clusters o unrelated sequences. (nih.gov)
  • Prediction of Protein Stability Changes is a structure-based method to predict the effects of missense variants on protein stability. (lu.se)
  • VariBench is a benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction. (lu.se)
  • More than 68 percent had less than 5 copies of the IS sequence suggesting that our local M.tuberculosis strains have a fewer number of copies compared to data shown in most countries. (who.int)
  • These methods had serious limitations in accuracy and reproducibility and never provided a reliable scheme for antigenic classification of strains. (medscape.com)
  • The Norovirus genus contains more than 40 different strains that are divided into 5 genogroups based on sequence similarity. (medscape.com)
  • Faster and more accessible DNA sequencing technologies have enabled, in the past decade, a large number of genomics and metagenomics projects focused on the microbial world [ 3 ]. (biomedcentral.com)
  • The resulting sequence data holds immense opportunities for the discovery of new microbial enzymes and their associated NPs [ 4 ]. (biomedcentral.com)