ProteinsGENOMICNucleotideGenomeResiduesNucleic acidsPeptideAlignmentPhylogeneticGenesAnalysesMutationsCharacterizationEncodesMutation2020EvolutionarySubcellularOriginateUnigenesAnalysisSpecificityMutantsPhylogenyCompositionStrainsBiologicalProtein sequenceModificationsSyntheticGeneticAssaysVariationDataEffectivelySearchesDisorderDiagnosisMoleculesDemonstrateStructureModelsInfectionMetabolic
Proteins16
- Alignment of the amino acid sequence of aprotinin with the Kunitz domains of human proteins allowed the identification and design of a family of peptides, named Angiopeps. (aspetjournals.org)
- 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)
- Results -Several proteins ranging in molecular mass from 55 to 75 kd were unique to the hemolytic strain. (avma.org)
- Methylated DNA affinity capture by methyl-CpG binding proteins produces fractions highly enriched for methylated DNA, suitable for coupling to next generation sequencing technologies. (biomedcentral.com)
- Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. (biomedcentral.com)
- A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. (biomedcentral.com)
- For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. (biomedcentral.com)
- Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. (biomedcentral.com)
- Therefore computational prediction of protein features from their sequence is often used for designing strategies for experimental characterization of proteins and is also important for genome annotation and drug target identification [ 4 , 5 ]. (biomedcentral.com)
- However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
- Most commonly, this approach leverages high-resolution mass spectrometric measurements of proteolyzed proteins, combined with tandem peptide fragmentation to match observed spectra with those expected from their amino acid composition. (biorxiv.org)
- 11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
- 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)
- These types of RNA help assemble protein building blocks (amino acids) into functioning proteins. (medlineplus.gov)
GENOMIC5
- Oligonucleotide primers, designed on the basis of amino acid sequences of 2 tryptic peptides derived from 1 such protein and conserved regions of the C and B genes from members of the repeats in the structural toxin (RTX) family of bacterial toxins, were used to amplify cytotoxin-specific genes from M bovis genomic DNA. (avma.org)
- An open reading frame encoding a 927-amino acid protein with a predicted molecular mass of 98.8 kd was amplified from M bovis genomic DNA. (avma.org)
- Currently, most protein sequences in databases are the result of translation of hypothetical transcripts derived from genomic sequencing data [ 3 ]. (biomedcentral.com)
- PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
- Furthermore, using sequence analysis of human genomic DNA, researchers concluded that the amino acids important for catalysis by COX-1 are conserved and are equally important for catalysis by COX-2. (medscape.com)
Nucleotide2
- The traditional phylogenetic principles and methods are based on amino acid or nucleotide sequence to assess homology, determine orthology and paralogy, and deduce relationships within gene families and/or reconstruct gene evolutionary events. (biomedcentral.com)
- The process or result of matching up the nucleotide or amino acid residues of two or more biological sequences to achieve maximal levels of identity and, in the case of amino acid sequences, conservation, for the purpose of assessing the degree of. (hupfburgen-funpark-candy-land.de)
Genome6
- One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. (virology.ws)
- As a result, extant angiosperms vary more than 1000-fold in genome sizes and nearly 50-fold in chromosome numbers [ 2 ]. (biomedcentral.com)
- Fortunately, with the availability of several fully sequenced plant genomes, studies of genome evolution and organization become possible in part by detecting syntenies and colinearities or clustering and ordering of neighboring matching gene pairs [ 3 ]. (biomedcentral.com)
- Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
- The full-length genome and genetic characterization of isolates were analyzed by Sanger sequencing. (biomedcentral.com)
- The complete genome of PCV2-GX-4, PCV2-GX-6, PCV2-GX-7, PCV2-GX-11 and PCV2-GX-16 have been amplified, sequenced, and deposited in GenBank (accession no. (biomedcentral.com)
Residues2
- Mutational analysis of CYP7B1 amino acid mutations related to hereditary spastic paraplegia type 5 considered phosphorylation, ligand/substrate binding and the structural roles of mutated amino acid residues, with R112, T297 and S363 mutations expected to have a direct impact on ligand binding, while mutations involving R417 would indirectly affect ligand binding as a result of impairment in catalytic function. (nih.gov)
- 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)
Nucleic acids1
- Samples were obtained from 28 different sites and extracted nucleic acids were treated with DNAase (to remove DNA genomes) and then reverse transcriptase (to copy RNA to DNA). (virology.ws)
Peptide2
- Exenatide is a synthetic version of exendin-4, a 39 amino acid peptide originally isolated from the venom of the Gila monster. (hindawi.com)
- These studies have combined peptide affinity pull-downs and quantitative mass spectrometry enabled by SILAC ( S table I sotope L abeling by A mino Acids in C ell Culture) [ 32 ]. (biomedcentral.com)
Alignment1
- Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
Phylogenetic2
- However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. (biomedcentral.com)
- Homology and phylogenetic analysis with reference strains showed that the isolates belonged to the PCV2d genotype. (biomedcentral.com)
Genes2
- each has drawbacks, especially when the sequences of the interested genes are truncated, contain gaps or are low quality [ 9 ]. (biomedcentral.com)
- Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in P. rockii . (biomedcentral.com)
Analyses2
- Based on these previous analyses and clinical findings, CLRN1 was directly sequenced in 17 patients susceptible to carrying mutations in this gene. (molvis.org)
- Procedures -For male goats, results of serum biochemical analyses collected from 1992 through 2003 were retrieved from computerized records, as were signalment, clinical diagnoses, and discharge status. (avma.org)
Mutations1
- After CLRN1 sequencing, we found two novel mutations, p.R207X and p.I168N. (molvis.org)
Characterization1
- We performed molecular characterization of the orthopoxvirus isolate by next-generation sequencing. (blogspot.com)
Encodes3
- Conclusions and Clinical Relevance -A gene was identified in M bovis that encodes a protein with sequence homology to other RTX toxins. (avma.org)
- The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
- Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
Mutation1
- Spontaneous mutation and acquired immunologic processes can result in this disorder, as well. (medscape.com)
20201
- v3 (Aug 2020): Paper thoroughly revised, with improved results and updated methodology. (biorxiv.org)
Evolutionary1
- 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)
Subcellular1
- In particular, the computational prediction of subcellular location from protein sequence information has been attempted mainly using three approaches. (biomedcentral.com)
Originate1
- He localized the biologic activity to a fraction of lipid soluble acids that he termed "prostaglandin," hypothesizing that these substances originate in the prostate gland. (medscape.com)
Unigenes1
- A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. (biomedcentral.com)
Analysis9
- New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing. (virology.ws)
- Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. (virology.ws)
- The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. (biomedcentral.com)
- The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis. (biomedcentral.com)
- PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
- 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)
- 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)
- Funk and co-investigators localized COX-1 to 9q32-q33.3 via somatic hybrid deoxyribonucleic acid (DNA) analysis. (medscape.com)
Specificity1
- have presented the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 Å resolution. (tcdb.org)
Mutants1
- To date, we have sequenced junctions from 23 rat mutants. (purdue.edu)
Phylogeny1
- ORF2-targeted gene sequencing is commonly used as a gold standard for phylogeny, epidemiology, and genotyping of PCV2 strains [ 5 ]. (biomedcentral.com)
Composition1
- Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. (biomedcentral.com)
Strains1
- The results of homology showed that PCV2-GX-6 was closely related to the reference strains PCV2-JS17-8 (GenBank accession no. (biomedcentral.com)
Biological1
- The resulting model contains information about biological properties in its representations. (biorxiv.org)
Protein sequence1
- However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
Modifications1
- The thiolate undergoes reversible (to sulfenic) or irreversible (to sulfinic and sulfonic acid) covalent modifications upon oxidation. (nature.com)
Synthetic1
- Regardless of the etiology, a deficiency of cyclooxygenase (COX), a key regulatory enzyme in the synthetic pathway of eicosanoid production, results in beneficial and detrimental physiologic conditions relative to imbalances of the eicosanoids. (medscape.com)
Genetic1
- This condition results from a combination of genetic, environmental, and lifestyle factors, many of which have not been identified. (medlineplus.gov)
Assays1
- Results of cytotoxin neutralization assays support the hypothesis that M bovis cytotoxin is encoded by this gene and belongs in the RTX family of bacterial exoproteins. (avma.org)
Variation1
- Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. (biomedcentral.com)
Data2
- In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. (biorxiv.org)
- That's scale - the amount of data I can afford to carry with me has changed dramatically, and as a result, my expectations about what's normal have changed. (scienceblogs.com)
Effectively2
- Exenatide shows 53% sequence homology with native GLP-1, while still binding effectively to GLP-1 receptor on pancreatic β cells for its insulinotropic effects. (hindawi.com)
- The results of qPCR showed that PCV2 can effectively proliferate in the liver, spleen, lung, and kidney. (biomedcentral.com)
Searches1
- Four remaining family members (MBD1, MBD2, MBD3 and MBD4) have been discovered on the basis of homology searches with the MeCP2 MBD amino acid sequence [ 8 ]. (biomedcentral.com)
Disorder1
- Hypochloridemic metabolic alkalosis was the most common acid-base disorder. (avma.org)
Diagnosis1
- Current hepatitis C virus (HCV) testing guidance recommends a two-step testing sequence for diagnosis of HCV infection. (cdc.gov)
Molecules1
- This damage results from a buildup of harmful molecules called reactive oxygen species, which are byproducts of energy production in mitochondria. (medlineplus.gov)
Demonstrate1
- Our results demonstrate that food restriction in S. jarrovii increases adrenocortical cellular rates of steroid production without affecting overall cellular sensitivity to ACTH. (bvsalud.org)
Structure1
- By 1964, after recognition of this basic structure, Bergstrom and colleagues successfully synthesized series 2 prostaglandins from arachidonic acid using sheep seminal fluid. (medscape.com)
Models1
- The results obtained with in vitro and in vivo models provided evidence for greater passage of aprotinin across the BBB than of holo-transferrin. (aspetjournals.org)
Infection2
- An orthopoxvirus infection was suspected because of negative-staining electron microscopy results. (blogspot.com)
- Co-infection with hepatitis B virus (HBV) and hepatitis D virus (HDV) results in hepatitis D, the most severe form of chronic viral hepatitis, frequently leading to liver decompensation and hepatocellular carcinoma. (cdc.gov)
Metabolic1
- The results revealed a comprehensive profile for metabolic activities among tissues, pointing to the equal importance of leaf, stem, and root in A. mongolicus for the production of bioactive compounds. (biomedcentral.com)