AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
Sequence Homology, Amino AcidAmino Acid SequenceAmino AcidsSequence Homology, Nucleic AcidMolecular Sequence DataCloning, MolecularBase SequenceSequence AlignmentAmino Acid SubstitutionSequence HomologyEscherichia coliDNA, ComplementaryBinding SitesDNAModels, MolecularRestriction MappingMutationProtein Structure, TertiaryGenesProtein ConformationAmino Acids, EssentialRecombinant ProteinsGenes, BacterialAmino Acid MotifsBacterial ProteinsSequence Analysis, DNAAmino Acid Transport SystemsPeptide FragmentsPlasmidsProtein BindingPhylogenyMolecular WeightSpecies SpecificityMutagenesis, Site-DirectedRNA, MessengerSubstrate SpecificityKineticsCell LineNucleic Acid HybridizationConserved SequenceOpen Reading FramesStructure-Activity RelationshipPeptidesRecombinant Fusion ProteinsDNA Restriction EnzymesProteinsCarrier ProteinsGene LibraryElectrophoresis, Polyacrylamide GelProtein Structure, SecondaryDNA, BacterialTranscription, GeneticDNA PrimersPolymerase Chain ReactionMultigene FamilyAmino Acids, AromaticSaccharomyces cerevisiaeLeucineCattleStructural Homology, ProteinAmino Acids, Branched-ChainBlotting, NorthernMembrane ProteinsAmino Acids, SulfurCyanogen BromideTrypsinsrc Homology DomainsChromatography, High Pressure LiquidChromosome MappingTransfectionCodonBlotting, SouthernViral ProteinsPlant ProteinsSequence AnalysisProtein BiosynthesisGene ExpressionGenes, ViralDNA-Binding ProteinsAlanineSequence DeletionMacromolecular SubstancesGenetic Complementation TestSequence Analysis, ProteinMutagenesisBiological EvolutionRepetitive Sequences, Nucleic AcidFungal ProteinsEvolution, MolecularLysineCOS CellsBiological TransportGenes, FungalCrystallography, X-RayChickensCysteineRabbitsRNADNA, ViralTranscription Factors
ProteinsAlignmentReceptorsMotifsGenomesSpecific amino acidGeneticsResiduesWhole-genome sequencesNucleic acidsCompletely sequencedSimilarityStructuralPeptideEnzymesGeneStructuresPolypeptideNucleotide sequenceMoleculePhylogeneticConsensus sequenceGenesEvolutionaryBioinformaticsSubstitutionAlignmentsResidueAntibodyComprisesViralSpeciesTranscriptQuantitativeMutationsSpiteAntigenTerminalDemonstrateProcessesSecondary structureDomain
Proteins6
  • The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. (biorxiv.org)
  • Structure and properties of proteins, nucleic acids, and their complexes. (keywen.com)
  • Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
  • Figure 1: The amino acid sequences for three small proteins. (customuniversitypapers.com)
  • A number of actin-binding proteins, including spectrin, alpha-actinin and fimbrin, contain a 250 amino acid stretch called the actin binding domain (ABD). (embl.de)
  • Proteins containing only a single amino terminal CH domain. (embl.de)
Alignment6
  • A relatively obvious approach to phylogenetic analysis of whole genomes is to extract as many genes as possible from the genome sequences, create a multiple sequence alignment from each of the genes and to concatenate all alignments. (biomedcentral.com)
  • SEquence-structure alignment with 123D+ server. (keywen.com)
  • The input to the program was the alignment between the target sequence and template structure(s). (keywen.com)
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)
  • Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, and the modeling of evolution. (limswiki.org)
  • Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)
Receptors1
  • Since most sequence variation associated with immunoglobulins and T cell receptors are found in the CDRs, these regions are sometimes referred to as hypervariable regions. (wikipedia.org)
Motifs1
Genomes4
  • Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. (biomedcentral.com)
  • Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
  • Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
  • Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. (limswiki.org)
Specific amino acid2
  • 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)
  • Proteases are enzymes that cut (cleave) polypeptides at specific amino acid sequences. (customuniversitypapers.com)
Genetics1
  • [3] [4] Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing . (limswiki.org)
Residues5
  • Two amino acids, Glu-16 and Tyr-19, were identified as key residues for binding and inhibition of Evasin-4. (unige.ch)
  • In vertebrates, rhodanese is a mitochondrial enzyme of about 300 amino-acid residues involved in forming iron-sulfur complexes and cyanide detoxification. (expasy.org)
  • It was discovered that the gene, called an early nodulin 40 (Enod40), previously annotated as transcribed with the formation of lncRNA encodes actually two short peptides (with a length of 12 and 24 amino acid residues) in plants, where they participate in the organogenesis of the root nodules [10, 11]. (fortunepublish.com)
  • Tertiary structure is formed by interactions among amino acid side chains and involves weak interactions including hydrophobic / hydrophilic interactions and hydrogen bonds, ionic bonds, and covalent bonds such as disulfide bridges formed between two cysteine residues. (customuniversitypapers.com)
  • If polypeptides from closely related species have the same amino acid sequence with the same amino acid residues at the same location, then treatment with the same enzyme should lead to synthesis of similar length fragments. (customuniversitypapers.com)
Whole-genome sequences2
  • Phylogenetic analysis using capsid gene and whole-genome sequences demonstrated that the isolates clustered with an IHHNV isolate from Ecuador. (cdc.gov)
  • As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
Nucleic acids2
  • The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)
  • With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)
Completely sequenced1
  • In addition, we have completely sequenced the viral genome of the SARS-CoV HSR1 and compared it to other SARS-CoV strains recently isolated in disease-epidemic areas. (cdc.gov)
Similarity2
  • Nucleotide sequences of PCR amplicons showed 99%-100% similarity to IHHNV isolates from Latin America and Asia. (cdc.gov)
  • The degree of similarity between sequences of amino acids. (lookformedical.com)
Structural5
  • Rhodanese homology domains are structural modules of about 120 amino acids, which occur in the three major evolutionary phyla [ 9 ]. (expasy.org)
  • Of these, LIF shows closest structural homology to granulocyte colony-stimulating factor and growth hormone (GH). (ox.ac.uk)
  • Results revealed the secondary, tertiary structural changes along with changes in free energy of folding, volume and accessible surface area. (uni-mysore.ac.in)
  • Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO. (lookformedical.com)
  • 1. A purified protease which comprises the amino acid sequence SEQ ID NO:1, or a functional equivalent thereof produced by conservative amino acid alterations which result in a protease which exhibits the same biological, biochemical, chemical, physical and structural properties of the protease of SEQ ID NO:1. (everypatent.com)
Peptide2
  • Corticotropin-releasing hormone (CRH) is a 41-amino acid peptide with noted sequence homology among species, specifically in the region required for biologic activity (amino-terminal region), and is a major secretagogue of pituitary corticotropin. (medscape.com)
  • On the basis of our results, a molecular model of peptide-bound NPRA was developed by homology modeling with the C-type natriuretic peptide- (CNP-) bound natriuretic peptide receptor C (NPRC) crystal structure. (hal.science)
Enzymes2
  • The C-terminal domain of the 990-amino acid Schizosaccharomyces pombe Spt5 protein, composed of repeats of a nonapeptide motif (consensus sequence TPAWNSGSK), is necessary and sufficient for binding to the capping enzymes in vivo (in a two-hybrid assay) and in vitro. (mskcc.org)
  • Using a homology search, we obtained a set of candidate sequences, modelled the tertiary structure of the selected enzymes, and compared them with experimental and model structures of known DAAOs. (actanaturae.ru)
Gene8
  • For this purpose, lip gene was amplified by conventional Polymerase Chain Reaction (PCR) and nucleotide sequence was analyzed in silico. (edu.pe)
  • The lip gene had 927 bp and mature protein, 284 amino acids. (edu.pe)
  • Finally, we note that sequence diversity in chromo domains may lead to diverse functions in eukaryotic gene regulation. (ox.ac.uk)
  • Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
  • We propose an approach that uses bioinformatic methods in combination with general 3D structure and active center structure analysis to confirm that the gene found encodes D-amino acid oxidase and to predict the possible type of its substrate specificity. (actanaturae.ru)
  • Based on an established filtering strategy and data analyses, along with confirmation by Sanger sequencing and co‑segregation, a novel frameshift mutation c.1317delA (p.Ala440LeufsTer14) in exon 10 of the APC gene was identified. (spandidos-publications.com)
  • For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
  • Here, we identified the coding sequence of the EZH2 gene and characterized its expression pattern in fetal tissues of Duroc pigs at 65- and 90-day postcoitus (dpc). (hindawi.com)
Structures5
  • Homology modeling is a computational method to build tertiary structures from amino-acid sequences. (wikipedia.org)
  • This involves the formation of bonds that lead to the proper folding of the polypeptide into secondary and tertiary structures. (customuniversitypapers.com)
  • Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures. (limswiki.org)
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. (limswiki.org)
  • Distinguishing three-dimensional structures characteristically formed by homologous protein sequences. (bvsalud.org)
Polypeptide5
  • The order of amino acids as they occur in a polypeptide chain. (lookformedical.com)
  • Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. (lookformedical.com)
  • A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. (lookformedical.com)
  • The overall three-dimensional structure of the polypeptide is the tertiary structure. (customuniversitypapers.com)
  • Thus, depending on which enzyme is used, and where the target amino acids are located, a polypeptide could be cut to generate different size fragments. (customuniversitypapers.com)
Nucleotide sequence1
Molecule1
  • Sequence analysis of the complete genome of SARS-CoV has shown an RNA molecule of about 29,750 bases in length, with a genome organization similar to that of other coronaviruses ( 9 - 11 ). (cdc.gov)
Phylogenetic1
  • Furthermore, the use of concatenated multiple sequence alignments discards information that can be utilised by other methods of phylogenetic inference. (biomedcentral.com)
Consensus sequence2
Genes4
  • Forty eight putative drought-induced WRKY genes were identified from a comparison between de novo transcriptome sequencing data of wheat without or with drought treatment. (biomedcentral.com)
  • Transcription factors, with specific DNA-binding domains (DBD) and trans -acting functional domains, can combine with specific DNA sequences to activate or inhibit transcription of downstream genes. (biomedcentral.com)
  • Difficulties with this approach may arise if orthologous genes cannot be identified with certainty or if the combined sequence length is still too small to give well-resolved trees. (biomedcentral.com)
  • Five Dmrt family genes with full-length transcript sequences were identified in Amur sturgeon. (researchsquare.com)
Evolutionary2
  • To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. (biorxiv.org)
  • that is, we can assess their evolutionary relationships based on these sequences. (customuniversitypapers.com)
Bioinformatics2
  • Arguably one of the first "bioinformatics" projects-though the concept didn't yet exist-involved the 1965 creation and maintenance of a protein sequence database called the Atlas of Protein Sequence and Structure by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. (limswiki.org)
  • Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
Substitution1
Alignments2
  • Sequence alignments for the functionally related molecules oncostatin M and ciliary neurotrophic factor, when mapped to the LIF structure, indicate regions of conserved surface character. (ox.ac.uk)
  • Sequence-structure alignments Sequence-structure alignments were generated and tested both at the sequence level as well as at the 3D level. (keywen.com)
Residue1
Antibody1
  • The tertiary structure of an antibody is important to analyze and design new antibodies. (wikipedia.org)
Comprises1
Viral2
  • This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death. (cnrs.fr)
  • The full-length viral genome sequence was similar to those derived from the Hong-Kong Hotel M isolate. (cdc.gov)
Species1
  • 11] Because of homology among species, human and ovine sequences are both used to stimulate pituitary production and adrenal cortisol production. (medscape.com)
Transcript1
  • In this study, we identified a transcript variant of EZH2 in porcine fetal tissues by cloning and sequencing. (hindawi.com)
Quantitative1
  • Quantitative real-time PCR (qRT-PCR) analysis showed that TaWRKY1 was slightly up-regulated by high-temperature and abscisic acid (ABA), and down-regulated by low-temperature. (biomedcentral.com)
Mutations1
  • The purpose of the present study was to report the clinical features of a Chinese family with FAP and screen for novel mutations using the targeted next‑generation sequencing technology. (spandidos-publications.com)
Spite2
  • is composed of two domains which, in spite of a negligible sequence homology, are characterized by very similar three dimensional folds. (expasy.org)
  • In spite of this similar organization, the SARS-CoV RNA sequence is only distantly related to that of previously characterized coronaviruses ( 9 ). (cdc.gov)
Antigen1
Terminal1
  • A 116-amino acid fragment of the guanylyl-transferase Pce1 suffices for binding to the Spt5 C-terminal domain (CTD) but not for binding to the Po1-II CTD. (mskcc.org)
Demonstrate2
  • while docking analysis with lipases substrates allowed to demonstrate the amino acids that participate in the binding pocket. (edu.pe)
  • We demonstrate that the distinct FK linker sequences per se do not account for lack of potentiation activity by FKBP51. (unboundmedicine.com)
Processes1
  • In higher eukaryotes - vertebrates and especially in mammals, the main role of DAAO is to maintain a certain level of D-amino acids, which are regulators of many important processes, primarily nervous activity. (actanaturae.ru)
Secondary structure1
  • Further the mutated protein secondary structure is predicted and tertiary structure is predicted using homology modeling. (uni-mysore.ac.in)
Domain6
  • We also developed a profile which covers the entire rhodanese homology domain. (expasy.org)
  • no information about the properties of the sequences is given through supervision or domain-specific features. (biorxiv.org)
  • We also present evidence that the HPV-18 E1 DNA-binding domain does not share the same nucleotide and amino acid requirements for specific DNA recognition as BPV-1 and HPV-11 E1. (cshl.edu)
  • Kunitz-like domain"--A protease inhibitor similar to soybean trypsin inhibitor or a nucleic acid sequence encoding a protease inhibitor which is similar to the soybean trypsin inhibitor. (everypatent.com)
  • A calponin homology domain is predicted in yeasst Cdc24p. (embl.de)
  • In canine epidermolysis bullosa acquisita, the immunoglobulin G (IgG) autoantibodies also target the type VII collagen noncollagenous (NC1) domain, which shares greater than 80% homology in amino acid sequence with the human NC1 domain. (medscape.com)