• includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain. (yeastgenome.org)
  • PB1-F2 Gene serogroup 1, we performed sequence- ence laboratories and sharing of based typing (SBT) ( 3 ) of 6 genes results. (cdc.gov)
  • Methods A next-generation sequencing (NGS) panel was created for the human TRPV1 gene and in addition, for the leukotriene receptors BLT1 and BLT2 recently described to modulate TRPV1 mediated sensitisation processes rendering the coding genes LTB4R and LTB4R2 important co-players in pharmacogenetic approaches involving TRPV1. (researchgate.net)
  • The NGS workflow was based on a custom AmpliSeq™ panel and designed for sequencing of human genes on an Ion PGM™ Sequencer. (researchgate.net)
  • A cohort of 80 healthy subjects of Western European descent was screened to evaluate and validate the detection of exomic sequences of the coding genes with 25 base pair exon padding. (researchgate.net)
  • This identified approximately 140 chromosome loci where nucleotides deviated from the reference sequence GRCh37 hg19 comprising the three genes TRPV1, LTB4R and LTB4R2. (researchgate.net)
  • It is suitable for large-scale sequencing of TRPV1 and functionally related genes. (researchgate.net)
  • The reports on base sequences of spider silk protein genes have gained importance as the mechanical properties of silk fibers have been revealed. (bioone.org)
  • Genes control everything from hair color to blood sugar by telling cells which proteins to make, how much, when, and where. (livescience.com)
  • Genes also include regulatory sequences. (livescience.com)
  • Although scientists don't fully understand their function, regulatory sequences help turn genes on. (livescience.com)
  • There are 4 major subfamilies of emm genes, which are defined by sequence differences within the 3' end, encoding the peptidoglycan-spanning domain. (medscape.com)
  • The proteins are produced under instruction from genes. (edu.au)
  • Switching different genes on or off affects which particular proteins are produced. (edu.au)
  • It is the sequence of bases that makes the instructions within genes. (edu.au)
  • Here, we present a phylogenomics-based approach for the identification of orthologous and paralogous genes in human, mouse, fly, and worm, which forms the foundation of the comparative analyses of the modENCODE and mouse ENCODE projects. (biorxiv.org)
  • The very premise of using model organisms to inform human biology relies on the fact that many biological processes, and the underlying genomic elements that encode them, are frequently conserved across large evolutionary distances, especially for protein-coding genes. (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)
  • Bioinformatics strategies were used to find other homologous genes and proteins, which can also degrade HCH present in various bacteria for controlling of pollution and offer clue to prevent its entry in the food chain. (ispub.com)
  • Genes are segments of deoxyribonucleic acid (DNA) that contain the code for a specific protein that functions in one or more types of cells in the body or the code for functional ribonucleic acid (RNA) molecules. (msdmanuals.com)
  • Protein synthesis is controlled by genes, which are contained on chromosomes. (msdmanuals.com)
  • Genes vary in size, depending on the sizes of the proteins or RNA for which they code. (msdmanuals.com)
  • Marshall Nirenberg, Har Gobind Khorana, and their colleagues, were the first to determine the genetic code and show how the nucleic acid bases, with their alphabet made up of A, U, G, and C, determine the sequence of the 20 different amino acids during protein synthesis. (github.io)
  • Watson and Crick were the first to realize that the seemingly random sequence of the four bases in DNA formed a code which specified the order of the twenty amino acids that make up most proteins. (github.io)
  • They found that their synthetic RNA specified that phenylalanine, an amino acid, be added to the end of a growing strand of linked amino acids, the precursor to proteins. (github.io)
  • Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. (yeastgenome.org)
  • somewhat similar sequences of about 110 amino acids each. (wikipedia.org)
  • BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. (ucsc.edu)
  • Some of these mutations change single protein building blocks (amino acids) in euchromatic histone methyltransferase 1. (medlineplus.gov)
  • from random sequences of amino acids is addressed. (lu.se)
  • ments of the amino acids along the protein chains. (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)
  • 1 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou 510632, China. (nih.gov)
  • The availability of accurate structure-based sequence alignments of protein families and superfamilies is crucial to inferring their evolutionary relationships, functional properties4 and to understand the structural variances between the different classes of proteins. (researchsquare.com)
  • Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
  • Our results indirectly support the theory that p16 expression is negatively regulated by the functional Rb protein. (nih.gov)
  • Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. (biomedcentral.com)
  • Some mutations may only affect a single codon, changing a single amino acid in a protein, therefore the protein may remain functional. (a-levelnotes.co.uk)
  • Microbial communities cluster at the structural- and functional potential-level based on the presence/absence of a disinfectant residual. (biomedcentral.com)
  • These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
  • functional proteins. (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)
  • The tests used for protein C testing can include enzyme-linked immunosorbent assay (ELISA), chromogenic assays, and the activated partial thromboplastin time (aPTT)-based functional protein C assay. (medscape.com)
  • An ELISA measures protein C immunological levels with very high sensitivity but cannot detect functional defects. (medscape.com)
  • Chromogenic assays can detect low levels of protein C with high sensitivity and can detect most functional defects. (medscape.com)
  • The aPTT-based functional protein C assay may yield misleadingly low protein C levels in the presence of (1) a factor V Leiden mutation and some other causes of activated protein C resistance, (2) elevated plasma factor VIII levels, or (3) hyperlipidemia. (medscape.com)
  • In addition, patients with lupus anticoagulants or those on direct thrombin inhibitors may have falsely normal results from an aPTT-based functional assay. (medscape.com)
  • The main aim of the course is to enable students to acquire specialised knowledge and understanding of membrane biochemistry and the molecular structure, topology and functional mechanisms of membrane proteins. (lu.se)
  • A number of proteins from each process, for which the structure is known, are explored in greater detail in order to highlight the functional molecular mechanisms. (lu.se)
  • We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
  • Profiles generated using structure-based sequence alignments of distantly related proteins at the family or superfamily level could be utilized to predict the fold of hypothetical sequences through profile-sequence search method is another success in the structure prediction area. (researchsquare.com)
  • PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/ . (biomedcentral.com)
  • Alternative approach to protein structure prediction based on sequential similarity of physical properties. (rochester.edu)
  • Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
  • Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)
  • Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.org)
  • Hence, we suggest a protocol that permits the reliable sequence alignment of distantly related proteins whose structural information is available. (researchsquare.com)
  • The method proposed is clearly suited to work for protein structural members with distant relationships. (researchsquare.com)
  • This structure-based sequence alignment protocol can be employed for a single superfamily or for a large number of structural domain superfamilies in a near-automatic and rapid manner. (researchsquare.com)
  • Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
  • This review aims to link recent molecular data, often translated into amino acid sequences and predicted three dimensional structural motifs, to known mechanical properties. (bioone.org)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
  • The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleavage are not well known. (biomedcentral.com)
  • Histones are structural proteins that attach (bind) to DNA and give chromosomes their shape. (medlineplus.gov)
  • Cells depend on their DNA for coding information to make various classes of proteins that include enzymes, certain hormones, transport proteins, and structural proteins that support life. (cdc.gov)
  • In contrast, hybridoma-based systems for producing monoclonal antibodies are subject to genetic drift and instability, increasing the potential for lot-to-lot variability or loss of antibody expression. (cellsignal.com)
  • Other may have no effect on protein structure due to the genetic code being degenerate. (a-levelnotes.co.uk)
  • The traditional Lancefield classification system, which is based on serotyping, has been replaced by emm typing, which has been used to characterize and measure the genetic diversity among isolates of S pyogenes . (medscape.com)
  • Genetic sequences of the bases are read in groups of three (called a triplet), with a possibility of 64 configurations or "words" in which to code information. (cdc.gov)
  • The genetic code is the sequence of DNA (base pairs) that tells a cell how to build proteins, the essential building blocks of life. (cdc.gov)
  • The sequence of base pairs of DNA molecules is the genetic blueprint of any living being. (lu.se)
  • This is followed by experimental determination using genetic construction and expression of a fusion protein of the membrane protein and a marker protein in a bacterial system which is subsequently analysed. (lu.se)
  • We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. (nih.gov)
  • At the ribosome, the processed mRNA is translated to produce proteins from amino acid units. (cdc.gov)
  • Deciphering protein–protein interactions. (crossref.org)
  • Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
  • Identification of protein-protein interactions (PPIs) is important for understanding how proteins work together in a coordinated fashion in a cell to perform cellular functions. (nature.com)
  • Even for Arabidopsis , known PPI data cover interactions with only about 34.55% of proteins. (nature.com)
  • Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions. (scilifelab.se)
  • A DNA molecule forms a double-helix where the complementary interactions between bases strike a balance between stability (protecting the integrity of the double helix) and accessibility (for instance, the bases need to be accessible when reading the DNA sequence). (lu.se)
  • However a publicly available, high-throughput meta-server is needed to combine the existing annotation tools from their disparate domains in efforts to support genome-scale sequence annotations, whereby a single-user interface can be used to access a variety of computational tools and the results from these tools. (biomedcentral.com)
  • We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. (rochester.edu)
  • Conclusions Results suggested that the NGS approach based on AmpliSeq™ libraries and Ion Personal Genome Machine (PGM) sequencing is a highly efficient mutation detection method. (researchgate.net)
  • Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. (scilifelab.se)
  • At some point in our distant past, someone got a mutation that caused a base to go missing in their A gene. (thetech.org)
  • Other companies are interested in sequencing to understand antimicrobial resistance, identify airborne pathogens and bioterror threats, and elucidate the relationship between a gene mutation and disease. (genengnews.com)
  • While these servers provide the convenience of a whole genome annotation, they do not accept protein sequences as input and, therefore, cannot run analyses on a set of pre-selected proteins from a given genome or a set of un-related proteins from multiple genomes. (biomedcentral.com)
  • That combination of speed, portability, and affordability puts real-time, whole-genome sequencing within reach of any scientist in the world. (genengnews.com)
  • MekB from Pseudomonas veronii and CgHle from Corynebacteriumglutamicum belong to the superfamily of α/β-hydrolase fold proteins. (rcsb.org)
  • sequences that fold well are isolated. (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)
  • Enzymes are complex proteins that control and carry out nearly all chemical processes and reactions within the body. (msdmanuals.com)
  • Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. (nih.gov)
  • Time scales of water dynamics at biological interfaces: peptides, proteins and cells. (lu.se)
  • Furthermore, based on sequence analysis of the Wnt-5a protein, I identified two peptides with Wnt-5a mimicking ability. (lu.se)
  • d2o5fa_ d.113.1.2 (A:) Hypothetical protein DR0079 {Deinococcus radiodurans str. (berkeley.edu)
  • BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. (ucsc.edu)
  • Dataset 6 is subset of the DATASET 3 extracted by clustering the protein sequences in dataset 3 based on their sequence similarity using CD-HIT suite (Huang et al. (lu.se)
  • Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. (rochester.edu)
  • In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.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)
  • The aim of this project is to explore quantum computing based methods for solving lattice protein problems. (lu.se)
  • Lectures dealing with methods for theoretical modelling of membrane protein structure, fusion protein techniques, X-ray crystallography, heterologous expression, solubilisation and purification of membrane proteins are also included in the course. (lu.se)
  • Determination of the transmembrane topology of a protein starts with a model of the protein based on sequence information and theoretical methods. (lu.se)
  • Epigenetic modifications are chemical changes to DNA and to certain proteins, called histones, that DNA wraps around. (edu.au)
  • We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. (nature.com)
  • Recently, metagenomics a new approach to identify culturable and non culturable bacteria with the help of 16S rDNA sequences isolate total DNA from HCH contaminated soil and amplified 16S rDNA through universal primers and confirmed its total population with denaturing gradient gel electrophoresis and sequencing. (ispub.com)
  • Zaragoza outbreak were identified at Christine Campese,§ nary analysis of 336 PB1 sequences the Spanish Reference Laboratory as and Carmen Pelaz* from GenBank ( 2 ). (cdc.gov)
  • Cases were identified in 31 (48%) of Colorado's 64 coun- sequencing (WGS) is performed by the CDPHE laboratory, ties. (cdc.gov)
  • The bacitracin disc test is simple to perform and interpret in an office-based laboratory and is sufficiently accurate for presumptive identification of GAS. (medscape.com)
  • The diagnosis may be suspected based on the patient history, physical examination, and laboratory findings. (medscape.com)
  • 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)
  • Accurate sequence alignments of distantly related proteins are crucial for the better understanding of proteins at their family/superfamily level. (researchsquare.com)
  • However, such alignments of distantly related proteins are often hard to obtain by automatic multiple sequence alignment programs. (researchsquare.com)
  • This protocol employs two stages of structure-based sequence alignments in order to obtain reliable alignments. (researchsquare.com)
  • We have earlier shown that the large-scale alignments of several protein domain superfamilies are possible by resorting to structure-based sequence alignment methods13-15. (researchsquare.com)
  • High quality of sequence alignments are crucial for comparative modeling and docking in computing and for the design of rational experiments. (researchsquare.com)
  • The alignments of protein sequences are required for the organization and assimilation of vast amounts of data. (researchsquare.com)
  • Rapid structure-based sequence alignments employ a comparison of the orientations of the secondary structures (Murthy20, SSAP7,21, and SEA22 programs) or hexapeptide fragments (DALI5,6) to recognize accurate alignments of protein domains that belong to the same superfamilies. (researchsquare.com)
  • It may miss more divergent or shorter sequence alignments. (ucsc.edu)
  • Histone acetyltransferases (HATs), histone methyltransferases and histone deacetylases (HDACs) and histone demethylases that modify histone proteins. (edu.au)
  • DNA methyltransferases, which modify certain bases in DNA, and a set of proteins including TET proteins that undo these modifications. (edu.au)
  • The protein sequence is 295 base pairs. (wikipedia.org)
  • The promoter is 1125 base pairs long, located between 48024511-48025635. (wikipedia.org)
  • A DNA sequence is a specific lineup of chemical base pairs along its strand. (livescience.com)
  • Most people with Kleefstra syndrome are missing a sequence of about 1 million DNA building blocks (base pairs) on one copy of chromosome 9 in each cell. (medlineplus.gov)
  • In it, two strands, composed of sugar (deoxyribose) and phosphate molecules, are connected by pairs of four molecules called bases, which form the steps of the staircase. (msdmanuals.com)
  • During extraction of DNA from cells, usually the DNA molecules get fragmented into pieces of size 105-106 base pairs. (lu.se)
  • Because of the non-covalent nature of the bonds between bases, the DNA molecules "melt" (base pairs get separated) when heated above room temperature. (lu.se)
  • The associated melting curve (fraction of "melted" DNA base pairs as a function of temperature) is sensitive to DNA sequence, with local melting temperatures that range from 60 to 110 °C. The sensitivity of DNA melting to DNA sequence can be used in DNA fingerprinting. (lu.se)
  • By performing optical measurements, the fraction of melting base pairs as a function of temperature can be extracted. (lu.se)
  • Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. (nih.gov)
  • Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. (nature.com)
  • Figure 2: N50 contig sizes from assemblies generated from sequence data for each sequencing platform. (nature.com)
  • In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)
  • Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. (yeastgenome.org)
  • Recently, Chen and ( fla A, pil E, asd , mip , momp S, and been more difficult without this tech- co-workers described the expression pro A) by using the protocol and data- nique in identifying the site where the of an 11th influenza A virus protein, base of EWGLINET. (cdc.gov)
  • Based on 30 SARS-CoV-2 RT-PCR-positive specimens from inpa- available data, seven (2%) vaccine breakthrough cases§§ were tients and outpatients to CDPHE for sequencing each week. (cdc.gov)
  • PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. (biomedcentral.com)
  • The large volume of sequencing data that are now available has created profound challenges in data transfer and analysis [ 3 ]. (biomedcentral.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)
  • The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids. (lu.se)
  • In our evidence-based table and recent highlights of the year , we have mentioned an increasing number of genomic tests and applications for which evidence-based recommendations exist and can save lives today. (cdc.gov)
  • 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)
  • We developed number of models using various types of features and achieved maximum accuracy of 66% using binary profile of nucleotide sequence taken from 5p arm of hairpin. (biomedcentral.com)
  • it is generally believed that all the copies in an organism are identical or nearly identical in nucleotide sequence. (ispub.com)
  • The lectures address the three different main types of membrane proteins and associated cellular processes: transport and transporters, signal transduction and receptors, bioenergetics and photosynthetic and respiratory proteins. (lu.se)
  • Dynamic and conformational switching in proteins. (rochester.edu)
  • The correct targeting and insertion of tail-anchored (TA) integral membrane proteins is critical for cellular homeostasis. (caltech.edu)
  • PPIs are essential for individual protein functions, forming various cellular pathways, and are also involved in the development of diseases. (nature.com)
  • Proteins perform most life functions, and make up almost all cellular structures. (livescience.com)
  • Specialized cell structures called ribosomes are the cellular organelles that actually synthesize the proteins (RNA transcription). (cdc.gov)
  • Multiply aligned set of sequences serve as convenient models to depict evolutionary drifts and provide convenient frameworks for mapping allied information such as secondary structures and functionally important residues. (researchsquare.com)
  • 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)
  • In search for global principles that may explain the organization of the space of all possible proteins, we study all known protein sequences and structures. (aaai.org)
  • All 4670 clusters were then compared using either a structure metric (when 3D structures are known) or a novel sequence profile metric. (aaai.org)
  • Since protein structures have a much higher degree of conservation than the sequences2, comparison of protein structures may reveal distant evolutionary relationships that would not be detected from sequence information alone3,4. (researchsquare.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)
  • This model, hereafter formation of three-dimensional protein structures. (lu.se)
  • Proteins are not just building blocks for muscles, connective tissues, skin, and other structures. (msdmanuals.com)
  • We have developed a series of novel approaches to protein biophysics based on ideas from information theory and sign. (rochester.edu)
  • Nonlinearities in protein space limit the utility of informatics in protein biophysics. (rochester.edu)
  • Gene mutations are changes to the base sequence or quantity of DNA within a gene or section of DNA. (a-levelnotes.co.uk)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • A newly described form, GSD type Ic, does not appear to be related to mutations within the transporter protein. (medscape.com)
  • Silks are composed principally of proteins with a predominance of alanine, serine and glycine and silk proteins are able to undergo irreversible transformations from soluble protein to insoluble fibres. (bioone.org)
  • In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work. (nih.gov)
  • In this paper we present a global map of the protein space based on our analysis. (aaai.org)
  • This organization extends our ability to predict the structure and function of many proteins beyond what is possible with existing tools for sequence analysis. (aaai.org)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Confocal immunofluorescent analysis of HeLa cells, insulin-treated (left) and LY294002-treated (#9901, right), using Phospho-S6 Ribosomal Protein (Ser240/244) (D68F8) XP ® Rabbit mAb (Alexa Fluor 488 ® Conjugate) (green). (cellsignal.com)
  • In this paper, we describe a new high-throughput, genome-wide analysis tool for deriving enzymatic functions and other annotations for protein sequences. (biomedcentral.com)
  • Reverse sequence analysis showed that the MLLT1 gene was fused to the 16p11.2 region. (cancerindex.org)
  • formed a Fourier analysis based on the random walk represen- erties in terms of thermodynamical and kinetic behavior, tation. (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)
  • Analysis of protein dynamics simulations by a stochastic point process approach. (lu.se)
  • In silico exercise addressing potential problems concerning the detection of heterologously expressed membrane proteins, solubilisation and evaluation of detergent properties, ion exchange chromatography and gel filtering in the presence of a detergent, and control of the protein's stability and integrity after purification. (lu.se)
  • Different cells in our body function in distinct ways because of variations in the proteins made by each cell. (edu.au)
  • Earlier studies systematically analyzed sequence variations in human pri-miRNAs/pre-miRNA and experimentally discovered that single nucleotide polymorphisms (SNPs) in miR-125a obstruct the processing of pri-miRNA to pre-miRNA [ 16 ]. (biomedcentral.com)
  • The sequence identity cut-off was kept at 30% and the sequence with the highest number of variations was chosen to represent each cluster. (lu.se)
  • This dataset has altogether 1592 variations on 272 proteins in human and non-human sequences. (lu.se)
  • Within the gene sequence 9 exons are present. (wikipedia.org)
  • The protein-making instructions come from short sections called exons. (livescience.com)
  • Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. (scilifelab.se)
  • TA proteins are defined by a hydrophobic transmembrane domain (TMD) at their C-terminus and are targeted to either the ER or mitochondria. (caltech.edu)
  • By curating TA proteins with experimentally determined localizations and assessing hypotheses for recognition, we bioinformatically and experimentally verify that a hydrophobic face is the most accurate singular metric for separating ER and mitochondria-destined yeast TA proteins. (caltech.edu)
  • DNA is composed of alternating sugar and phosphate groups, with the sugar attached to 1 of 4 possible nucleotide bases (adenosine, cytosine, guanine, thymidine). (cdc.gov)
  • These bases attach to each other in a specific pattern: adenosine:thymidine and cytosine:guanine. (cdc.gov)
  • We examined the expression of p16 and Rb protein by means of immunohistochemistry in 61 non-small cell lung cancers and have demonstrated an inverse relationship between the expression of p16 and Rb protein: 28/30 specimens that did not stain for p16 stained for Rb and 21/31 p16-positive specimens did not stain for Rb. (nih.gov)
  • Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. (biomedcentral.com)
  • PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome. (biomedcentral.com)
  • In recent years, a number of publicly available meta-servers have been developed for protein sequence annotation [ 6 - 8 ], but public access to these servers is often restricted to a limit that ranges from 1 to 10 protein sequences per HTTP request. (biomedcentral.com)
  • As a result, the localization of many TA proteins are misclassified by the simple heuristic of overall hydrophobicity. (caltech.edu)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • Other representative plant species cover even less protein involved in known PPIs. (nature.com)
  • This locus is not translated into a protein. (yeastgenome.org)
  • This system is based on a sequence at the 5' end of a locus ( emm ) that is present in all isolates. (medscape.com)
  • As originally described by Lancefield, beta-hemolytic streptococci can be divided into many groups based on the antigenic differences in group-specific polysaccharides located in the bacterial cell wall. (medscape.com)
  • Despite the availability of several structure-based sequence alignment procedures (DALI5,6, SSAP7, CE8, 3DCOFFEE9, MUSTANG10 etc.) in the public domain, we have observed, from our large-scale construction of aligned protein domain superfamilies13-15 that a huge amount of manual intervention is required for the choice of initial equivalences, in dealing with distantly related multiple members. (researchsquare.com)
  • Beyond Supersecondary Structure: Physics-Based Sequence Alignment. (rochester.edu)
  • 2017). In this dataset, we identified and characterized the Liver-Specific Protein 2 (LISP2) protein as an early molecular marker of liver stage development. (elifesciences.org)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • Advances in next generation sequencing technologies have enabled rapid generation of newly sequenced genomes at a rate that can no longer be handled by a single-core non-distributed computing system in a feasible manner [ 1 , 2 ]. (biomedcentral.com)
  • A larger version of the MinION instrument, the GridION, is even being used to sequence the genome of the tulip-at 34 Gb, it is one of the largest genomes around. (genengnews.com)
  • The communication between molecular motors and double-stranded DNA binding proteins is a common feature in DNA replication, repair, recombination and transcription and also in instances where conflict occurs between these processes. (sciencedaily.com)
  • 120 credits) in Chemistry and Molecular Biology and compulsory for a degree of Master of Science (120 credits) in Protein Science. (lu.se)
  • The displayed sequence can be downloaded in FASTA format as a .txt file. (yeastgenome.org)
  • A metric focusing on an 11 residue segment of the TMD performs well when classifying human TA proteins. (caltech.edu)
  • Accurate whole human genome sequencing using reversible terminator chemistry. (nature.com)
  • For example, with a human dna search, 20 is minimum matches required, based on the genome size, to filter out lower-quality results. (ucsc.edu)
  • There are many phosphorylation sites found on the protein, mostly on serine and threonine. (wikipedia.org)
  • An individually planned and executed minor project during two weeks, in which the students express a membrane protein of their choice and demonstrate in some way that the expression was successful. (lu.se)