• Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids. (umassmed.edu)
  • Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. (wikipedia.org)
  • It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding motif present in the nuclear high-mobility-group proteins HMG1 and HMG2. (nih.gov)
  • The serotype has been identified since 1996 as a frequent nucleotide sequences in genes encoding three rotavirus cause of severe disease in hospitalized children from many proteins, VP7, VP8, and NSP4, but they were distinct from countries, including the United States, Japan, India, G9P[8] strains isolated in previous years. (cdc.gov)
  • Phylogenetic analysis characterized the sequences into two discrete clusters representing two of the four global lineages of human G1 VP7 proteins. (microbiologyresearch.org)
  • The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
  • This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins. (duke.edu)
  • DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. (lookformedical.com)
  • The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
  • This four and a half-credit course will present an introduction to the Biophysical Chemistry and Structural Biology of proteins and nucleic acids. (columbia.edu)
  • Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
  • PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
  • To under- denoted the AB model, consists of chains of two kinds of stand the statistical distribution of hydrophobicity along proteins ``amino acids'' interacting with Lennard-Jones potentials. (lu.se)
  • Northern blot analysis and S1 protection and mapping experiments have revealed that the mRNA for MLCK is 5.5 kilobases in length, but there also exists a second mRNA of 2.7 kilobases that shares a high degree of homology with about 520 base pairs at the 3' end of the cDNA for MLCK. (torvergata.it)
  • The highest degree of homology in the Cox 1 nucleic acid sequences and predicted amino acid sequences was found between A. agkistrodontis and A. armillatus . (unl.edu)
  • The degree of homology between target and probe results in stable hybridization. (enzolifesciences.com)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • The genome of Aspergillus oryzae , a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. (nature.com)
  • Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
  • Syntenic analysis of the three aspergilli revealed the presence of syntenic blocks and A. oryzae -specific blocks of sequence (lacking synteny with the two other aspergilli) in a mosaic manner throughout the A. oryzae genome ( Fig. 1 ). (nature.com)
  • Thus, the increase in genome size seems to be due to an A. oryzae lineage-specific acquisition of sequence, rather than loss of sequence in A. nidulans and A. fumigatus . (nature.com)
  • This suggests that the genome size differences are largely due to sequence acquisition in A. oryzae . (nature.com)
  • Topics covered include various high-throughput genomics technologies (genome sequencing, DNA microarrays, proteomics), quantitative modeling of transcriptional and post-transcriptional regulatory networks, synthetic biology, and the world of RNA structure, dynamics, and function. (columbia.edu)
  • In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia . (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)
  • Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. (biomedcentral.com)
  • High frequency intra- and intermolecular recombination among large repeated sequences is the rule, generating a heterogeneous pool of genome configurations within a single individual [ 12 - 14 ]. (biomedcentral.com)
  • Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. (cdc.gov)
  • Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. (cdc.gov)
  • Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (cdc.gov)
  • Due to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. (ox.ac.uk)
  • We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. (ox.ac.uk)
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor. (wikipedia.org)
  • citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
  • The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
  • The env genes contain a cis-acting RNA target sequence for the rev protein (= GENE PRODUCTS, REV ), termed the rev-responsive element (RRE). (lookformedical.com)
  • The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
  • Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. (nature.com)
  • Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. (unboundmedicine.com)
  • In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. (biomedcentral.com)
  • Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (bvsalud.org)
  • Dimerized STATs then translocate to the nucleus, where they bind DNA in the promoter sequences of target genes to activate transcription. (medscape.com)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
  • To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. (unboundmedicine.com)
  • Hel-N1, a human RNA-binding protein, shares significant homology with Drosophila protein ELAV, which is essential for fly neuronal development. (duke.edu)
  • The derived amino sequence was found to contain a region of high homology (54%) to the rabbit skeletal muscle enzyme and also very significant homology (35%) to the catalytic subunit of phosphorylase b kinase and cGMP-dependent protein kinase. (torvergata.it)
  • Peptide nucleic acid (PNA) amphiphiles: synthesis, self-assembly, and duplex stability. (umassmed.edu)
  • a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. (sbgrid.org)
  • Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. (cdc.gov)
  • Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
  • Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. (wikipedia.org)
  • For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)
  • permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)
  • Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (wikipedia.org)
  • The term "percent homology" is often used to mean "sequence similarity", that is the percentage of identical residues (percent identity), or the percentage of residues conserved with similar physicochemical properties (percent similarity), e.g. leucine and isoleucine, is usually used to "quantify the homology. (wikipedia.org)
  • Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
  • As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution, or, as with shorter sequences, by chance, meaning that they are not homologous. (wikipedia.org)
  • The genomic component of the CRISPR-Cas system is formed by a series of variable spacers, which in some cases share sequence similarity with viruses, plasmids, or bacteria. (pjmonline.org)
  • The degree of similarity between sequences. (bvsalud.org)
  • an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles. (sbgrid.org)
  • Bit-parallel sequence-to-graph alignment. (cdc.gov)
  • 14. Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. (rjpdft.com)
  • Areas that will be covered include: sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
  • Sequences are either homologous or not. (wikipedia.org)
  • Homologous sequence regions are also called conserved. (wikipedia.org)
  • Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (wikipedia.org)
  • This affinity and complementary sequence allow binding to specific regions of a target sequence of nucleotides. (enzolifesciences.com)
  • In developing a probe, a sequence of nucleotides must be identified, isolated, reproduced in sufficient quantity, and tagged with a label that can be detected. (enzolifesciences.com)
  • Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). (umassmed.edu)
  • Many new nucleic acid-based diagnostic tools or assays have been developed that allow analysis of DNA and RNA molecules in clinical samples. (enzolifesciences.com)
  • In theory, any nucleic acid can be used as a probe provided it can be labeled to permit detection and quantitation of the hybrid molecules formed between the probe and sequence to be identified. (enzolifesciences.com)
  • SHERLOCK: nucleic acid detection with CRISPR nucleases. (cdc.gov)
  • A unique feature of the CRISPR-Cas system is that it provides adaptive and hereditary immunity against foreign nucleic acids, mim-icking in some ways the immune systems of eukaryotes. (pjmonline.org)
  • These regions are interspaced with repeat sequences that are identical or almost identical within a single CRISPR cassette. (pjmonline.org)
  • These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods. (wikipedia.org)
  • The DNA sequences of the LTRs were compared in phylogenetic analyses with LTRs from 22 other ETn-related sequences. (essex.ac.uk)
  • NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (ncbs.res.in)
  • Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. (wikipedia.org)
  • Based on the 18S rRNA sequence, the shortest hereditary distance was found between A. agkistrodontis and Raillietiella spp. (unl.edu)
  • Twenty-nine strains (representing 79% of the complete collection) were further identified by 16S rRNA gene sequencing, rpoB gene sequencing and DNA-DNA hybridizations. (ilvo.be)
  • The restriction analysis and partial sequencing of the gene shows that it contains (1) four alternatively spliced exons previously described in rodent and bovine but not in human tau cDNAs and (2) two CpG islands, one associated with the promoter region, the other with exon 9. (nih.gov)
  • Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)
  • Sequence analysis of two tumors failed to reveal any structural changes within exon 1, as found by others in Burkitt's lymphoma. (lu.se)
  • Sequencing and analysis of Neanderthal genomic DNA. (uchicago.edu)
  • Sequence analysis revealed that FPR2 is 69% identical in sequence to the human NFPR and shares extensive homology to several other chemoattractant receptors. (unm.edu)
  • The course includes a series of biophysical research-related topics including practical introductions to the software tools available for the visualization and modeling of biomolecular structures and the bioinformatic analysis of biomolecular sequence and structural homology. (columbia.edu)
  • 11. Szklarz, G.D., Halpert, J.R. Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450. (rjpdft.com)
  • In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
  • wavelength corresponding to -helix structure, as one might have statistical analysis on the sequences that fold well indicates expected, but also at large wavelengths. (lu.se)
  • Such partial homology may result from a gene fusion event. (wikipedia.org)
  • Understanding mechanisms underlying human gene expression variation with RNA sequencing. (uchicago.edu)
  • A DNA probe is a labeled fragment of DNA that contains a nucleotide sequence specific for the gene or chromosomal region of interest. (enzolifesciences.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)
  • False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. (uchicago.edu)
  • The influence of the local sequence environment on RNA loop structures. (mpg.de)
  • The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. (biomedcentral.com)
  • It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. (biomedcentral.com)
  • Considering that the number of non redundant amino acid sequence entries is around 408,000 http://www.expasy.org/sprot/ , there is a huge gap between known annotated sequences and available 3 D structures. (biomedcentral.com)
  • MODELLER is one of the most widely used tools for homology or comparative modeling of protein three-dimensional structures. (biomedcentral.com)
  • or nucleic acid or in the structure of an organ that reflects a common evolutionary origin. (wormclassroom.org)
  • He also noted concern regarding delays in referring specimens to the laboratory for testing, and emphasized the need for improvement in timeliness of reporting and tracking of the viruses referred for genomic sequencing. (who.int)
  • He thanked the regional and global specialized laboratories for their efforts to provide timely results of the genomic sequencing of wild polioviruses, and for their help in planning and monitoring polio eradication activities in the Region. (who.int)
  • Additionally, in San Diego County, nucleic acid amplification tests (NAATs) are used to test for urethral, pharyngeal, and rectal gonorrhea and chlamydia infections at the county's public health laboratory. (cdc.gov)
  • Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (wikipedia.org)
  • Genetic distance calibration with the fossil record estimated the pairwise sequence divergence as 0. (unboundmedicine.com)
  • These aberrant transcripts are the products of abnormal RNA splicing and termination owing to the inserted sequence, and transcription initiation within the 3' long terminal repeat (LTR) of the ETn. (essex.ac.uk)
  • DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
  • We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)
  • Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. (mpg.de)
  • Modeling RNA loops using sequence homology and geometric constraints. (mpg.de)
  • MODELLER is a program for automated protein Homology Modeling. (biomedcentral.com)
  • In this context, the development of various user friendly and accurate tools for homology modeling is an active area of research such as new recent tools like HHPRED and Modeller at http://toolkit.tuebingen.mpg.de/sections/tertstruct toolkit, GeneSilico https://genesilico.pl/toolkit/ [ 9 - 15 ]. (biomedcentral.com)
  • EasyModeller is a standalone tool with a very intuitive interface which clearly defines the different steps of homology modeling (Additional file 1 ). (biomedcentral.com)
  • The ultimate goal of protein modeling is to predict a structure from its sequence with accuracy equivalent to the best experimentally obtained results. (rjpdft.com)
  • Homology Modeling and Generation of 3D-structure of Protein. (rjpdft.com)
  • All of these homologies were found in the known catalytic domains of these enzyme, thus enabling us to predict the location of the catalytic domain for the chicken gizzard myosin light chain kinase. (torvergata.it)
  • A sequence family database built on ECOD structural domains. (uni-trier.de)
  • Phosphorylated STATs dimerize within the cytosol via their phosphotyrosines and Src-homology 2 (SH2) domains. (medscape.com)
  • Two small repeats of 516 and 604 bp, respectively, have been cloned and sequenced. (elsevierpure.com)
  • The geno-mic component is a DNA loci containing short frag-ments of targeted nucleic acid sequences (spacers) inter-spaced by short repeated sequences (repeats). (pjmonline.org)
  • The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers. (uni-trier.de)
  • Nucleic Acid Heteroduplexes" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
  • An algorithm for selection of functional siRNA sequences. (dbcls.jp)
  • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. (uchicago.edu)
  • Homologies between human and dolphin chromosomes detected by heterologous chromosome painting. (tamu.edu)
  • Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1. (dbcls.jp)
  • Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. (wikipedia.org)