• Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (embl.de)
  • It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 2 in that it contains acidic N-terminal amino acid residues. (lookformedical.com)
  • Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (embl.de)
  • A sophisticated high-order framework nucleic acid (FNA) was engineered for the targeted delivery and responsive release of environment tolerant antisense peptide nucleic acids (asPNAs). (bvsalud.org)
  • Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. (bvsalud.org)
  • The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. (bvsalud.org)
  • Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. (bvsalud.org)
  • OBJECTIVES: To examine the bactericidal effect of antisense peptide-peptide nucleic acids (P-PNAs) that can block the expression of DNA gyrase or topoisomerase IV in FQ-resistant Escherichia coli (FRE). (bvsalud.org)
  • We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)
  • The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. (lu.se)
  • The goal is to assign acquired spectra to known peptide sequences and potential co- and post-translational modifica- tions. (lu.se)
  • The need to keep track of protein modifications is readily recognized by the proteomics community, and few repositories of known peptide modifications have been created. (lu.se)
  • Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms. (wikipedia.org)
  • The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. (lookformedical.com)
  • In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. (nature.com)
  • The best method for examin- evolution of groups of genes, and assemble information from ing M. tuberculosis complex genotyping data gathered over genome sequencing projects. (cdc.gov)
  • Deep sequencing has revealed thousands of eukaryotic protein-coding genes that defy the central dogma, producing circular noncoding RNAs rather than linear messenger RNAs. (bcm.edu)
  • For some genes, the abundance of the circular RNA exceeds that of the associated linear mRNA by a factor of 10, raising the interesting possibility that the function of some protein-coding genes may actually be to produce circular noncoding RNAs, not proteins. (bcm.edu)
  • Using RNAi screening in Drosophila cells, we identified many hnRNPs, SR proteins, core spliceosome, and transcription termination factors that control the outputs of reporter and endogenous genes. (bcm.edu)
  • In total, these results indicate that inhibition or slowing of canonical pre-mRNA processing events shifts the steady-state output of protein-coding genes towards circular RNAs, which likely helps explain why and how circular RNAs show tissue-specific expression profiles. (bcm.edu)
  • In addition, ASP-gyrA3 and ASP-parC2, which bind to the FRE-specific coding sequence within the gyrA and parC structural genes, respectively, showed selective bactericidal effects against FRE isolates. (bvsalud.org)
  • Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis. (lookformedical.com)
  • To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. (biomedcentral.com)
  • Multiple alignments of protein sequence families indicate residues that are more conserved than others, and the points at which insertions and deletions are more frequent. (biopred.net)
  • Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary. (wikipedia.org)
  • Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from alpha-actinin by an elongation process that included two duplications of a block of seven repeats. (embl.de)
  • In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. (nature.com)
  • Biopolymers include the polysaccharides such as cellulose, starch, the carbohydrate polymers produced by bacteria and fungi and animal protein-based biopolymers such as wool, silk, gelatin and collagen: biopolymers, especially the carbohydrate origin, have been found very promising industrial application in … This group consists of naturally occurring polymers and chemical modifications of these polymers. (cichlidresearch.com)
  • During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis. (biopred.net)
  • In this review, I will explain what HMMs are, describe their strengths and limitations, and highlight how HMM-based profiles are beginning to be used in protein structure prediction and large-scale genome sequence analysis. (biopred.net)
  • Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bond. (wikipedia.org)
  • We examined spoligotype data using a bioin- formatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. (cdc.gov)
  • Profiles' of protein structures and sequence alignments can detect subtle homologies. (biopred.net)
  • Within the HMM formalism, it is possible to apply formal, fully probabilistic methods to profiles and gapped sequence alignments. (biopred.net)
  • These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl.de)
  • OTEs are undesired changes to genomic DNA sequences with some sequence similarity to the target site. (idtdna.com)
  • OTEs occur when the Cas enzyme is directed to the wrong site by the gRNA due to such sequence similarity. (idtdna.com)
  • The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. (biomedcentral.com)
  • Computational analysis is increasingly important for inferring the functions and structures of proteins [1] because the speed of DNA sequencing has long since surpassed the rate at which the biological function of sequences can be elucidated experimentally. (biopred.net)
  • Biopolymer definition is - a polymeric substance (such as a protein or polysaccharide) formed in a biological system. (cichlidresearch.com)
  • Almost any sequence can now be efficiently circularized in eukaryotic cells, which has enabled us (and others) to begin to ask how circular RNAs function. (bcm.edu)
  • This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. (biomedcentral.com)
  • 7. In a eukaryotic cell, protein synthesis occurs in the A. nuclear envelope. (nursingdons.com)
  • Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
  • The genomes of several other phytopathogenic species in the Magnaporthales have thereafter been sequenced 8 . (nature.com)
  • The paucity of studies and the lack of sequence data from non-model species in Magnaporthales results in a poor understanding of the phylogeny and an unstable taxonomy of Magnaporthales species. (nature.com)
  • To this end, we recently sequenced the genomes of five species and generated transcriptomes from 21 species of Magnaporthales, including saprobes and plant pathogens 9 . (nature.com)
  • The method can be used for automated detection of chemical/post- translational modifications, quality control of experiments and labelling approaches, and to control the modification settings of protein identification tools. (lu.se)
  • The secondary structure is responsible for the shape that the nucleic acid assumes. (wikipedia.org)
  • Spectrin repeats [ ( PUBMED:8266097 ) ] are found in several proteins involved in cytoskeletal structure. (embl.de)
  • Although mechanistically simple, this step occurs in a highly selective manner, as the sequence of the repeats can drastically alter the efficiency of circular RNA production. (bcm.edu)
  • When CRISPR genome editing was introduced in 2009, plasmids were generously made available by the labs where they were developed so that other researchers around the world could use them to express Cas proteins in CRISPR experiments. (idtdna.com)
  • The success of proteomics experiments, such as studies of protein function and cell signaling pathways, ultimately de- pends on how well the protein content in samples is identified and annotated. (lu.se)
  • Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. (wikipedia.org)
  • It is this linear sequence of nucleotides that make up the primary structure of DNA or RNA. (wikipedia.org)
  • Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. (wikipedia.org)
  • The present status of erythrocyte spectrin structure: the 106-residue repetitive structure is a basic feature of an entire class of proteins. (embl.de)
  • A 'profile' (defined as a consensus primary structure model consisting of position-specific residue scores and insertion or deletion penalties) is an intuitive step beyond the pairwise sequence alignment methods. (biopred.net)
  • Polymers, including biopolymers, are made of repetitive units called monomers.Biopolymers inherently have a well defined structure: The exact chemical composition and the sequence in which these units are arranged is called the primary structure. (cichlidresearch.com)
  • Groundbreaking work in biochemistry has led to our knowledge of the structure of DNA, RNA and proteins and it holds the promise of further breakthroughs in treatment in the future. (hud.ac.uk)
  • In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the internal repeat in spectrin occurs several times. (embl.de)
  • When repeat sequences from the flanking introns base pair to one another, the splice sites are brought into close proximity and backsplicing occurs. (bcm.edu)
  • Hidden Markov models are a general statistical modeling technique for 'linear' problems like sequences or time series and have been widely used in speech recognition applications for twenty years. (biopred.net)
  • Pairwise sequence comparison methods such as BLAST and FASTA generally assume that all amino acid positions are equally important even though a great deal of position-specific information is usually available for a protein or protein family of interest. (biopred.net)
  • from Int J Paediatr Dent 2000 Dec;10(4):328-34) The X-linked form is also known as Zinsser-Cole-Engman syndrome and involves the gene which encodes a highly conserved protein called dyskerin. (lookformedical.com)
  • This analysis shows how a modular protein unit can be used in the evolution of large cytoskeletal structures. (embl.de)
  • Sequence logo analysis suspected TB transmission and suspected laboratory cross- can find motifs in potentially related nucleic acid or protein contamination. (cdc.gov)
  • Logo analysis combines these data on a select regions was used to evaluate if genotyping every new graphic that illustrates the location and degree of sequence patient isolate from a particular region was useful. (cdc.gov)
  • We applied sequence direct DNA fingerprinting studies are relatively simple to logo analysis to find motifs based on the presence or absence design, we are still learning how best to use in toto the large of specific spacer sequences. (cdc.gov)
  • Consequently, a lot of effort is put into identifying the constituent proteins using mass spectrometric methods. (lu.se)
  • such as Mycobacterium africanum (8,9), M. bovis (10), and the We suggest using the sequence logo technique to under- W-Beijing family (11,12). (cdc.gov)
  • There are three potential metal binding groups on nucleic acids: phosphate, sugar, and base moieties. (wikipedia.org)
  • Inhalation Toxicology Downloaded from informahealthcare.com by CDC Information Center on 07/06/12 alternative to methyl bromide as a fumigant, there is potential here as a sequence of key events and processes, starting for human exposures to MeI. (cdc.gov)
  • One is faced with a number of difficult problems: what are the best ways to set the position-specific residue scores, to score gaps and insertions, and to combine structural and multiple sequence information? (biopred.net)
  • The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. (nature.com)
  • The complete taxonomic breakdown of all proteins with SPEC domain is also avaliable . (embl.de)
  • In this study, we sequenced the complete genome of Nautilus pompilius in the hope of providing a critical reference for the evolution of cephalopods. (nature.com)
  • We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. (biomedcentral.com)
  • These approaches promise to enable researchers to assess, on a large scale, both expression level and functional state of the proteins that carry out most functions in a cell. (lu.se)
  • These approaches depend on sequence databases that are used by the engines to match real spectra to theoretical in silico spectra. (lu.se)
  • We showed that repetitive elements, e.g. (bcm.edu)
  • and Public Health Research Insti- differentiation achieved with each spacer sequence. (cdc.gov)
  • Integrated DNA Technologies acquires Archerâ„¢ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
  • At the same time, sentinel surveillance of sequences (15). (cdc.gov)
  • An increase of a single percentage point may mean learning something useful about an additional 700 human proteins by the time elucidation of the sequence of the human genome nears completion round about the year 2002. (biopred.net)
  • A ubiquitously expressed telomere-binding protein that is present at TELOMERES throughout the CELL CYCLE. (lookformedical.com)
  • In addition, S. fibuligera was cultivated alone on starchy waste in Czechoslovakia or in mixed culture with Candida utilis on potato-processing wastes in Sweden to produce single-cell protein, which was used for protein supplementation in animal feeds [ 10 ]. (biomedcentral.com)
  • There are 257395 SPEC domains in 23741 proteins in SMART's nrdb database. (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing SPEC domain in the selected taxonomic class. (embl.de)
  • Established sequence comparison algorithms detect significant similarities between known database sequences and 35-80% of new proteins, depending on the organism. (biopred.net)
  • PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. (bvsalud.org)
  • Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. (idtdna.com)
  • Taxonomic distribution of proteins containing SPEC domain. (embl.de)
  • stand the distribution of each spacer sequence used in the spo- ligotype assay. (cdc.gov)
  • The key idea is that an HMM is a finite model that describes a probability distribution over an infinite number of possible sequences. (biopred.net)
  • Each state then emits symbols according to that state's emission probability distribution, creating an observable sequence of symbols. (biopred.net)
  • Starting from some initial state, a sequence of states is generated by moving from state to state according to the state-transition probabilities until an end state is reached. (biopred.net)
  • We now know that the evolution of multidomain proteins has frequently involved genetic duplication events. (embl.de)