Protein and nucleic acid sequence sequence analysis dna. Medical search. Frequent questions

The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new transcription factor binding sites (TFBS) recognition algorithms. (wikipedia.org)
They amplified and sequenced 200-bp to 10,000-bp fragments from 15 genomic locations, spanning 35 MYXV genes, and demonstrated that it was highly (97%-100% identity) similar to Lausanne. (cdc.gov)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
Genes are simply sequences of nucleic acid (DNA in humans) that code for a protein. (extremetech.com)
Subsequent genomic sequence analysis of multiple genes including elongation factor 3, a component of fungi protein synthesis not found in protozoa, further supported this notion. (medscape.com)
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. (nih.gov)
Based on the phylogenetic analysis and structural characteristics, 197 identified bHLH genes could be well classified into 21 groups. (biomedcentral.com)
For the first time, a comprehensive analysis identified the bHLH genes in Chinese white pear and demonstrated that PbrbHLH195 is involved in the production of ROS in response to cold stress, suggesting that members of the PbrbHLH family play an essential role in the stress tolerance of pear. (biomedcentral.com)
The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. (ncsu.edu)
The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. (ncsu.edu)
mRNA steady state levels of the chlorophyll a/b-binding protein of photosystem II, ferredoxin I, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 and pEA207, two other light-responsive genes, were determined during chlorophyll photooxidation. (ncsu.edu)
In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and, consequently, expression of target genes. (biomedcentral.com)
A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. (researchsquare.com)
have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
The assembly was characterized, including analyses of the genomic structure, with the aim of providing data to support the discovery of beneficial or harmful genes and to improve our understanding of the molecular pathogenesis. (researchsquare.com)
In addition, using sequences of three mitochondrial genes, the phylogenetic relationships between every sample with a known karyotype were determined, which revealed significant nucleotide divergence among the karyomorphs. (scielo.br)
Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. (columbia.edu)
F2 contains 6550 variants randomly sampled from the set of common human SNVs without clinical assertion associated with protein-coding genes in F1. (lu.se)
F3 contains 770 variants as a validation set including 70 SNVs in 'positive' set in non-coding regions of protein-coding genes newly reported and 700 randomly sampled common human variants, matched per type of region to the 'positive' set. (lu.se)

Polymerase chain reaction (PCR) is a powerful core molecular biology technique that is an efficient and rapid in vitro method for enzymatic amplification of specific DNA or RNA sequences from various sources. (sigmaaldrich.com)
Using thermal cyclers, there are three stages during each amplification cycle, including denaturing double-stranded DNA (dsDNA) into separate single stranded DNA, annealing primers to the target DNA sequence, and extension, where DNA polymerase extends the DNA from the primers, creating new dsDNA with one old strand and one new strand. (sigmaaldrich.com)
This method for routine PCR amplification of DNA uses standard Taq DNA polymerase. (sigmaaldrich.com)
Molecular genetic tests for detecting drug-resistance are, in general, just a variation of nucleic acid amplification (NAA) tests and can reliably provide information on the presence of mutations associated with drug resistance in 1 to 2 days. (cdc.gov)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
An automated rapid nucleic acid amplification test called Xpert MTB/RIF has been recommended by the World Health Organization (WHO) for the diagnosis of tuberculous meningitis. (msdmanuals.com)

Purification and restriction endonuclease analysis of plant nuclear DNA. (ncsu.edu)
Topics covered will include high-throughput assay development, screening, chemical library creation, high-throughput chemistry, affinity purification of target proteins and target validation, protein microarrays, molecular evolution, protein engineering and synthetic biology. (columbia.edu)

TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. (wikipedia.org)
The content of the database is organized in a way that it is centered around the interaction between transcription factors (TFs) and their DNA binding sites (TFBS). (wikipedia.org)
TESS (Transcription Element Search System) - analyzes sequence similarities with binding sites of TRANSFAC as well as potential binding sites using the matrix libraries of TRANSFAC and three other sources. (wikipedia.org)
Transcription factors (TFs) are protein molecules with special structure and function of regulating gene expression, which plays many crucial roles in plant growth and development [ 1 ]. (biomedcentral.com)
Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. (ncsu.edu)
The ratio between AR1 RNA and the major leftward RNA was constant and was used to normalize AR1 transcription for viral DNA copy number. (ncsu.edu)
A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. (ncsu.edu)
Here we present analysis of transcription factor binding motifs co-localized with non-coding variants. (biomedcentral.com)
Further analysis of transcription factors with conserved binding motifs can reveal cell regulatory pathways crucial for the survivability of various human cancers. (biomedcentral.com)
Sequence motifs are small sequences capable of acting as binding sites for a particular transcription factor [ 1 ]. (biomedcentral.com)
Transcription factors are specific proteins that bind to distinct sites on the genome. (biomedcentral.com)
Biochemical processes as diverse as the elastic response of DNA, protein-induced DNA bending, chromosomal segregation, replication, transcription, translation, protein translocation across membranes, catalyzed protein and nucleic acid folding and unfolding, and even the ubiquitous processes of induced-fit molecular recognition, are all examples in which forces and torques develop in molecules as they move along their reaction coordinates. (berkeley.edu)
In prokaryotes, and specially in eukaryotes, replication and transcription regulation involve the interaction of many specialized protein factors at regulator locations on the sequence to ensure correct sequence recognition, initiation, processivity, fidelity, and kinetic control. (berkeley.edu)

Analyses of chlorophylls a and b and the chlorophyll a/b-binding protein suggest that accumulation of the protein and its mRNA are coordinated with chlorophyll abundance at several steps. (ncsu.edu)
In addition to post-transcriptional regulation at the level of mRNA and protein stability, there may exist coordination at the transcriptional stage. (ncsu.edu)
Phytochrome Regulation of Greening in Pisum: Chlorophyll Accumulation and Abundance of mRNA for the Light-Harvesting Chlorophyll a/b Binding Proteins. (ncsu.edu)
We compared time courses, escape from reversal by far-red light, and fluence-response behavior for induction of mRNA for the light-harvesting chlorophyll a/b binding proteins (Cab mRNA) with those for induction of rapid chlorophyll accumulation in seedlings of Pisum sativum cv Alaska. (ncsu.edu)
Therefore, the level of Cab mRNA, as measured by the presence of sequences hybridizing to a cDNA probe, does not limit the rate of chlorophyll accumulation after transfer of pea seedlings to white light. (ncsu.edu)
The Drosophila Nanos protein is a localized repressor of hunchback mRNA translation in the early embryo, and is required for the establishment of the anterior-posterior body axis. (embl.de)
Characterization of cDNA clones for human myeloperoxidase: predicted amino acid sequence and evidence for multiple mRNA species. (rusmedserv.com)
Concordance of p16(INK4a) and E6*I mRNA among HPV-DNA-Positive Oropharyngeal, Laryngeal, and Oral Cavity Carcinomas from the ICO International Study. (who.int)

In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. (wikipedia.org)
The terminal regions of human chromosomes are known to contain specialised DNA sequences and may be vulnerable to rearrangements causing human genetic diseases and particularly idiopathic mental impairment. (bmj.com)
Many genetic variations outside protein-coding regions are associated with maize phenotypes. (nature.com)
Computational studies and Bioinformatics is an interdisciplinary field that progresses and applies computational methods to explore biological data collections such as protein samples, cell populations and genetic sequences for newer predictions or find out new Biology. (wikicfp.com)
CRISPRs are genetic elements containing direct repeats separated by unique spacers, many of which are identical to sequences found in phage and other foreign genetic elements. (berkeley.edu)
Using a combination of biochemical, structural, and genetic approaches, we found that Cas1 and Cas2 functions as a protein complex. (berkeley.edu)
In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)

The company's latest advancement, Caris Assure™ , is a blood-based, circulating nucleic acids sequencing (cNAS) assay that combines comprehensive molecular analysis (Whole Exome and Whole Transcriptome Sequencing from blood) and serial monitoring - making it the most powerful liquid biopsy assay ever developed. (carislifesciences.com)
Typically, PCR is used to amplify a target sequence followed by a second assay to determine if the sequence contains a mutation associated with resistance. (cdc.gov)
Detection of Circulating HPV16 DNA as a Biomarker for Cervical Cancer by a Bead-Based HPV Genotyping Assay. (who.int)

Deciphering protein–protein interactions. (crossref.org)
The HLH domain promotes protein-protein interactions and allows the formation of homo-dimer or hetero-dimer complexes [ 7 ]. (biomedcentral.com)
In 'DNA-Protein Interactions: Principles and Protocols, Third Edition', this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. (nhbs.com)
Comprehensive and authoritative, 'DNA-Protein Interactions: Principles and Protocols, Third Edition' serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research. (nhbs.com)
Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Manon Gaudreault, Marie-Eve Gingras, Maryse Lessard, Steeve Leclerc, and Sylvain L. Guerin 3. (nhbs.com)
Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper Athanasios G. Papavassiliou 14. (nhbs.com)
These systems can be extremely divergent mechanistically and provide a rich area to research RNA:protein interactions, including novel protein folds. (berkeley.edu)
posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
We are studying the structural basis of protein-DNA interactions and their relevance in the processes of control of gene expression using single molecule manipulation methods. (berkeley.edu)

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)
ABSTRACT In order to define the protein expressional changes related to the process of meglumine antimoniate resistance in anthroponotic cutaneous leishmaniasis (CL), we performed a comparative proteomics analysis on sensitive and resistant strains of Leishmania tropica isolated from Iranian CL patients. (who.int)
The study shows the usefulness of proteomics in identifying proteins that may express differences between sensitive and resistant L. tropica isolates. (who.int)

In the 1980s, biochemical analysis of the nucleic acid composition of Pneumocystis rRNA and mitochondrial DNA identified the organism as a unicellular fungus rather than a protozoan. (medscape.com)
Studies using purified protein produced in yeast cells has confirmed the biochemical function of the SGT2 protein in SGA production as the UDP-glucose:solanidine glucosyl transferase. (usda.gov)
RNA-targeting CRISPR-Cas systems - We use biochemical activity assays in conjunction with structural techniques and sequencing to investigate RNA-targeting CRISPR systems, such as the Type VI effector, Cas13a. (berkeley.edu)

Proteins are the primary class of biological macromolecules and serve to carry out most cellular functions. (columbia.edu)

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 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)

RNA codons and protein synthesis. (crossref.org)
Facilities include those for protein-sequence analysis, peptide and oligonucleotide synthesis, access to the synchrotron at Lawrence Berkeley National Lab for X-ray crystallography, and NMR spectrometry. (berkeley.edu)
OBJECTIVE: Synthesis and in-silico studies of 4-Phenyl thiazol-2-amine derivatives as anti-breast cancer agents and molecular docking was used to assess the compounds' capacity to bind ER-α protein target. (bvsalud.org)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)

Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)

of nucleic acid structure (Westhof, 1988). (lu.se)

Derwahl M, Seto P, Rapoport B. Complete nucleotide sequence of the cDNA for thyroid peroxidase in FRTL5 rat thyroid cells. (rusmedserv.com)
Nucleotide sequence of the cDNA encoding mouse thyroid peroxidase. (rusmedserv.com)
30 bps) and have a typical nucleotide sequence, although there may normally be variations due to mutations that occurred because of the selective pressure that the genome has undergone over time [ 4 ]. (biomedcentral.com)
Moreover, speci®c hy- found in narrow minor groove regions in a variety dration patterns seem to play a role in nucleotide sequence recognition by proteins (Otwinowski of oligonucleotide duplexes (PriveÂ et al. (lu.se)

The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. (ncsu.edu)
The basic building blocks of the immune system are the large number and variety of antibodies, which are protein-based molecules created by cells to bind with and neutralize any harmful antigens. (biosave.com)
We will discuss the structure and function of both proteins and small molecules in biological systems. (columbia.edu)
Small organic molecules function in energy production and creating building blocks for the components of cells and can also be used to perturb the functions of proteins directly. (columbia.edu)
Develop the theoretical framework for the analysis and the interpretation of single molecules data including how to extract equilibrium data from non-equilibrium measurements. (berkeley.edu)
Usually, the NOE and NMRD in B-DNA is expected to be less ``integral'' than methods can only provide bounds on the residence water molecules buried inside proteins. (lu.se)

Most PTMs are catalyzed by highly specific protein modifying enzymes, which have some specific recognition motif. (deepdyve.com)
For instance, the Type I protein arginine methyltransferases are known to methylate a number of proteins that contain an arginine glycine glycine (RGG)-motif [6]. (deepdyve.com)
Exact approaches usually use the consensus sequence for motif representation, employing some mathematical optimization as the search model. (biomedcentral.com)

Caris Assure™ sequences the complete coding region of the gene as well as all the RNAs being expressed. (carislifesciences.com)

This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. (fsf.org)
Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences. (fsf.org)

Because molecular beacons can use different fluorophores, real-time PCR assays can be designed in which different DNA fragments or mutations can be amplified and detected simultaneously in the same tube. (cdc.gov)

RT-PCR products from six patients who died from TBE between 2013 and 2017 were directly sequenced and analysed phylogenetically. (who.int)

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. (embl.de)
There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)
They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)
We have developed an approach for detecting motifs in biopolymers sequences. (biomedcentral.com)

For instance, the SwissVariant database (http://swissvar.expasy.org/) contained 76 613 variants in 20 244 human proteins on 10 January 2018. (deepdyve.com)

The HLH region is located at the C-terminus of the bHLH domain, which consists of two parental α -helixes, mainly composed of hydrophobic residues, connected by a relatively dispersed (length and primary sequence) loop region. (biomedcentral.com)
PTMs are specific to types of amino acid residues. (deepdyve.com)
For example, phosphorylation mainly occurs on a subset of three types of amino acids, including serine (S), threonine (T) and tyrosine (Y). Methylation is predominantly found on lysine (K) and arginine (R) residues. (deepdyve.com)
Consequently, amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence PTM of protein and bring about a detrimental effect on protein function. (deepdyve.com)
where X can be any amino acid, and number indicates the number of residues. (embl.de)
These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. (embl.de)

Characterization of a chloroplast sequence-specific DNA binding factor. (ncsu.edu)

In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)

Reorganizing the protein space at the Universal Protein Resource (UniProt). (ecmdb.ca)

Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). (nature.com)
Techniques for measuring specific nucleic acid interaction with another nucleic acid or with a protein by digestion of the non-interacting nucleic acid by various nucleases. (bvsalud.org)

The conserved bHLH domain consists of about 60 amino acids and has two functional segments, the basic region and the HLH region. (biomedcentral.com)
For non-coding regions estimates of selection pressure can be based on functional annotation of sequence variants. (biomedcentral.com)
Prokaryotes have evolved a nucleic acid-based immune system that shares some functional similarities with RNA interference in eukaryotes. (berkeley.edu)
To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)
Our comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control. (researchsquare.com)
Gene-based association testing identified increased risk for iHLHS associated with variation in CAPN2 (p= 1.810(-5)), encoding a protein involved in functional adhesion. (cdc.gov)
4462 functional sequence variations in regulatory DNA regions in training dataset F1 and 1116 functional SNVs in test datasets F2. (lu.se)
ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. (lu.se)

The DNA sequence of the human X chromosome. (nih.gov)
Human thyroid peroxidase: complete protein sequence, chromosome mapping, and identification two alternately spliced mRNAs. (rusmedserv.com)

Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. (nih.gov)
Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart 9. (nhbs.com)
Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. (nhbs.com)
Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. (nhbs.com)
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. (lu.se)

Phylogenetic analysis of CRISPR-associated (Cas) proteins suggests there are at least seven distinct versions of this immune system. (berkeley.edu)
F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level. (researchsquare.com)

We employ traditional biochemistry, combined with sequencing, live-cell imaging, and structural biology approaches, to uncover the fundamental mechanisms driving the CRISPR effectors now being developed as genome editing and diagnostic tools. (berkeley.edu)
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)

This part shall carry 20 questions pertaining to General Science, Quantitative Reasoning & Analysis and Research Aptitude. (pathfinderacademy.in)
DTEM) has developed and coordinated a mixtures program that includes trend analysis to identify the mixtures most often found in environmental media, in vivo and in vitro toxicological testing of mixtures, quantitative modeling of joint action, and methodological development for assessment of joint toxicity. (cdc.gov)
We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)

In collaboration with Stanley Qi and the laboratories of Wendell Lim , Jonathan Weissman , and Adam Arkin , we pioneered the engineering of CRISPR-Cas proteins for new purposes by converting Cas9 into a tool for targeted control of gene expression, referred to as CRISPR interference (CRISPRi). (berkeley.edu)
In this platform, catalytically inactive Cas9 serves as an RNA-guided DNA binding protein to silence gene expression in a sequence-specific manner. (berkeley.edu)
In this lesson you will gain experience in performing omics data analysis by working through part of a bioinformatics pipeline for analyzing gene expression data. (r-bloggers.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

A standard PCR consists of target DNA, a set of synthetic oligonucleotide primers that flank the target DNA sequence, a thermostable DNA polymerase (usually Taq polymerase), and nucleotides. (sigmaaldrich.com)

and, regulation of biological processes such as chromosomal folding, protein secretion and intracellular signaling. (berkeley.edu)
Also, the analyses indicate that chromosomal rearrangements occurred independently within the distinct lineages of S . marmoratus complex, which resulted in the appearance of distinct karyotypic variants in a non-linear fashion related to diploid numbers and in the appearance of similar non-homologous chromosomes. (scielo.br)

Through comprehensive molecular profiling (Whole Exome and Whole Transcriptome Sequencing) and the application of advanced artificial intelligence (AI) and machine learning algorithms, Caris has created the large-scale clinico-genomic database and cognitive computing needed to analyze and unravel the molecular complexity of disease. (carislifesciences.com)
We performed exome sequencing on 331 families with iHLHS aggregated from four independent cohorts. (cdc.gov)

A comprehensive redevelopment of the ribosome profiling workflow involves improved nuclease treatment and sequencing library preparation, enabling richer and more accurate translatome profiling with lower input and fewer technical hurdles. (nature.com)
After all non-interacting regions are eliminated by nuclease digestion, the protected nucleic acid that remains is analyzed. (bvsalud.org)

85% and the method is applicable for maps with RNA-only, DNA-only and DNA-RNA-protein complex structures. (nature.com)
Stability of protein and nucleic acid structures. (pathfinderacademy.in)

Assessment of potential binding affinity changes induced by substitutions allows studying selection of sequence variants in binding sites in a way resembling usage of non-synonymous and synonymous substitutions in codons. (biomedcentral.com)
In collaboration with the laboratory of David Savage , we have also developed a series of high-throughput mutant library construction, screening, and sequencing pipelines to probe CRISPR-Cas protein function and to isolate engineered variants with novel properties. (berkeley.edu)

Frequencies of synonymous and non-synonymous substitutions allow studying selection of cancer somatic mutations in protein-coding regions [ 11 ]. (biomedcentral.com)
Digital PCR is an end-point PCR method that is used for absolute quantification and for analysis of minority sequences against a background of similar majority sequences, e.g., quantification of somatic mutations. (sigmaaldrich.com)

Computational mutation analysis can greatly narrow down the efforts on experimental work. (deepdyve.com)
It is a computational field that involves the analysis of complex omics data. (r-bloggers.com)

Few methods for three-dimensional structure modeling of nucleic acids from cryo-EM data exist. (nature.com)
The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
Our high quality reagents are available for every workflow, including popular DNA assembly methods such as NEBuilder ® HiFi DNA Assembly and NEBridge ® Golden Gate Assembly . (neb.com)
Author Manuscript class of cellular RNA for which the standard sequencing methods cannot yet be applied efficiently and quantitatively, although attempts have been made (e.g. ref 2). (cdc.gov)
The course covers the basics, principles and limitations for the most common methods for multivariate statistics (analysis of variance, principal component analysis and partial least squares regression), experimental design (super-saturated and factorial designs) and method validation with a focus on practical use. (lu.se)

This analysis leverages experimentally sequenced data and in silico mixtures to simulate transcript expression differences, which enables a performance assessment of long-read tools developed for isoform detection, differential transcript expression analysis and differential transcript usage analysis. (nature.com)
Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat. (ncsu.edu)
Human thyroid peroxidase (TPO) isoforms, and TPO-2: analysis of protein expression in Graves' tissue. (rusmedserv.com)

Membrane structure and function: Structure of model membrane, lipid bilayer and membrane protein diffusion, osmosis, ion channels, active transport, ion pumps, mechanism of sorting and regulation of intracellular transport, electrical properties of membranes. (pathfinderacademy.in)
Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G-protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two-component signaling systems, bacterial chemotaxis and quorum sensing. (pathfinderacademy.in)

The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. (fsf.org)
We begin with an introduction to bioinformatics and omics data analysis, and conclude with the walkthrough of a simple bioinformatics workflow for aligning transcriptomic sequences with genomic data. (r-bloggers.com)
The following graphic depicts a typical workflow for preparing, analyzing, and visualizing results from transcriptomic RNA sequencing data. (r-bloggers.com)

A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (nih.gov)

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. (fsf.org)

The first half of the course will cover protein structure and enzyme kinetics. (columbia.edu)
Author Manuscript and RNA repair protein AlkB-derived enzyme mixture was first used to remove methylations at the Watson-Crick face. (cdc.gov)

Analysis of the Escherichia coli genome. (ecmdb.ca)
The complete genome sequence of Escherichia coli K-12. (ecmdb.ca)
Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. (ecmdb.ca)

The Use of Diethyl Pyrocarbonate (DEPC) and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA Brenda F. Kahl and Marvin R. Paule 7. (nhbs.com)
Reactive probes for conjugations of DNA with proteins and peptides. (muni.cz)

Updates to Data Collections ------------------------------------ New databases have been added to the file server recently: (a) Steven Henikoff's BLOCKS database Henikoff, S. and Henikoff, J. G. (1991) Automated assembly of protein blocks for database searching. (bio.net)

Recently, we used a similar large-scale protein engineering and screening platform to construct circularly permuted, viral protease-activated ProCas9s that orchestrate programmed cellular responses to pathogen-associated protease activity. (berkeley.edu)

Cloning and sequence analysis of the human salivary peroxidase-encoding cDNA. (rusmedserv.com)

The members of this family are designated by a highly conserved domain called the bHLH which are able to bind and form DNA dimers [ 2 ]. (biomedcentral.com)
We show that full-length and C-terminal Nanos proteins bind to RNA in vitro with high affinity, but with little sequence specificity. (embl.de)

MFMD performance was assessed using ChIP-seq data retrieved from the JASPAR site, promoter sequences extracted from the ABS site, and artificially generated synthetic data. (biomedcentral.com)

CASC4 was named as a CAncer Susceptibility Candidate 4 , and now it's GOLM2 (golgi membrane protein 2). (extremetech.com)

Annealing is the process of heating and cooling two single-stranded oligonucleotides with complementary sequences. (sigmaaldrich.com)
The virion consists of a single-stranded RNA molecule enclosed by the core membrane and the envelope (E) protein. (who.int)

The Doudna lab employs protein engineering and screening strategies to bestow CRISPR-Cas enzymes with improved and novel functionalities. (berkeley.edu)

Anatomy5

Organisms22

Chemicals and Drugs86

Analytical, Diagnostic and Therapeutic Techniques and Equipment45

Phenomena and Processes90

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science14

Health Care8

Genes20

Amplification6

Purification2

Transcription13

MRNA8

Genetic7

Assay3

Interactions9

Proteomics3

Biochemical3

Biological macromolecules1

Homology2

Synthesis5

Amino Acid Seq1

19881

Nucleotide sequence4

Molecules6

Motif3

Caris Assure1

Alignments2

Fragments1

20171

Motifs4

20181

Residues6

Characterization1

Genomic sequence1

UniProt1

Interaction2

Functional8

Chromosome2

Identification5

Phylogenetic analysis2

Structural biology2

Quantitative3

Gene expression4

Oligonucleotide1

Chromosomal2

Exome2

Nuclease2

Structures2

Variants2

Mutations2

Computational2

Methods5

Expression3

Regulation2

Workflow3

High-throughput protein1

Genome Analysis1

Enzyme2

Escherichia3

Probes2

Assembly1

Viral1

CDNA1

Bind2

Promoter1

Membrane protein1

Single-stranded2

Enzymes1