Having a nucleotide sequence. Medical search. Frequent questions

The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. (wikipedia.org)
DDBJ is a member of International Nucleotide Sequence Database Collaboration (INSDC) . (nig.ac.jp)

Sequences of ribosome binding sites from the large size class of reovirus mRNA. (wikidata.org)
The purpose of these studies was to detect and determine the nucleotide sequences of mRNA enzymes germacrene A synthase (GAS, EC 4.2.3.23), germacrene A oxidase (GAO, EC 1.14.14.95) and costunolide synthase (COS, EC 1.14.13.120), involved in the biosynthesis of costunolide in A. glabella . (academicjournals.org)
Using specific primers, mRNA fragments of genes encoding sesquiterpene lactones biosynthesis enzymes were amplified and their nucleotide sequences were determined. (academicjournals.org)
Answer] During translation nucleotide base triplets (codons) in mRNA are read in sequence in the 5′ → 3′ direction along the mRNA. (answersmcq.com)
What amino acid sequence does the following mRNA nucleotide sequence specify? (answersmcq.com)

It involves the following computerized databases: NIG's DNA Data Bank of Japan (Japan), NCBI's GenBank (USA) and the EMBL-EBI's European Nucleotide Archive (UK). (wikipedia.org)
Other information about this group: The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community. (edu.au)
The contents of this collection is dynamic and will change over time as more data is deposited into the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt). (edu.au)

As a sub-objective, since PDE10A transcript variants were reported strictly through analyses of bovine genomic sequence, we also wanted to determine the nucleotide and amino acid sequences by experimental evidence. (plos.org)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)

While the standard BLAST program is widely used to search for homologous sequences in nucleotide and protein databases, one often needs to compare only two sequences that are already known to be homologous, coming from related species or, e.g. different isolates of the same virus. (nih.gov)
Zebedee, SL & Lamb, RA 1989, ' Nucleotide sequences of influenza A virus RNA segment 7: A comparison of five isolates ', Nucleic acids research , vol. 17, no. 7, pp. 2870. (northwestern.edu)
Genetic relatedness of the isolates was characterized by multilocus sequence typing. (frontiersin.org)
Most of these CRAB isolates (77.62%) were classified as clone complex 92 (CC92), and sequence type (ST) 92 was the most prevalent STs, followed by ST195, ST136, ST843, and ST75. (frontiersin.org)
Five of seven WN virus isolates showed 92-98% homology in the nucleotide sequence of their PCR products. (usuhs.edu)
No correlation was established between the degree of nucleotide homology, geographic location, time of isolation, or source of the isolates. (usuhs.edu)
Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. (who.int)
There were two different mismatches in the probe target sites of the HA gene sequences of all isolates ( n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT-PCR isolates. (who.int)

Design and test primers for this sequence using Primer-BLAST. (nih.gov)
The nested PCR primers used to isolate HCV sequences were designed and manufactured within CDC. (cdc.gov)

The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format. (nih.gov)
No BLAST database contains all the sequences at NCBI. (nih.gov)
Coding sequences (CDS) were predicted based on an in-house workflow that integrates ab initio predictions from Glimmer ( 10 ), Genemark ( 11 ), Prodigal ( 12 ), and Critica ( 13 ) with homology information derived from a BLAST search against NCBI nr ( 14 ). (asm.org)

It is known to act through protein phosphorylation via PRKA and through the activation of guanine nucleotide exchange factors like EPAC. (plos.org)

Since the 1990s, most of the world's major scientific journals have required that sequence data be deposited in an INSDC database as a pre-condition for publication. (wikipedia.org)
In many scientific journals, it is required to assign and to describe INSDC accession number for a nucleotide sequence on the research paper. (nig.ac.jp)
Once released, the nucleotide sequences submitted to INSDC including DDBJ are available for everyone . (nig.ac.jp)

The sequence had only one long open reading frame consisting of 239 codons, which was found to correspond to the spo0A gene by comparing the nucleotide sequence of the wild-type gene with those of the mutant alleles. (elsevierpure.com)
the alphabet is the 20 proteinogenic amino acids for proteins and the sense codons (i.e., the 61 codons that encode amino acids in the standard genetic code ) for aligned protein-coding gene sequences. (wikipedia.org)

The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Mollusca, commonly known as molluscs, mollusks. (edu.au)
Refer to the previous Export into protein sequences section on how to set the protein database file. (readthedocs.io)

The syntax is called INSDSeq and its core consists of the letter sequence of the gene expression (amino acid sequence) and the letter sequence for nucleotide bases in the gene or decoded segment. (wikipedia.org)
if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). (scienceopen.com)
Count the bases in a DNA sequence and return the results in a structure. (mathworks.cn)
Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. (lu.se)

The human HapMap constructed by single nucleotide polymorphisms (SNPs) provides efficient sequence variation information that can speed up the discovery of genes related to common diseases. (psu.edu)

Map 1: the map describes national viruses isolation, intratypic differentiation and nucleotide sequencing laboratories. (who.int)

Goupil S, Maréchal L, El Hajj H, Tremblay M-È, Richard FJ, Leclerc P (2016) Identification and Localization of the Cyclic Nucleotide Phosphodiesterase 10A in Bovine Testis and Mature Spermatozoa. (plos.org)

The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc. (bvsalud.org)

Direct determination of DNA nucleotide sequences: structure of a fragment of bacteriophage phiX172 DNA. (wikidata.org)
The mapping and sequence determination of the single site in phiX174am3 replicative form DNA cleaved by restriction endonuclease Pst I. (wikidata.org)
Direct determination of DNA nucleotide sequences. (wikidata.org)

The CDS/transcript files are usually associated with the proteome files in genome sequencing projects. (readthedocs.io)

The sequence of one isolate was virtually identical to the published sequence of the Nigerian isolate (99.5% homology). (usuhs.edu)

Small deletions remove one or a few nucleotides within a gene, while larger deletions can remove an entire gene or several neighboring genes. (medlineplus.gov)

We determined the complete nucleotide sequence of the 16S rRNA from a new bacterium collected from the surfaces of women's hands. (springeropen.com)
The morphology of an isolated bacterial strain was found to be rod type, and the bacterium was identified as Lactobacillaceae species based on the GenBank database, through a phylogenetic analysis using the 16S rRNA sequence. (springeropen.com)
In addition, 16S rRNA sequencing was conducted to identify the microorganisms isolated from human hands. (springeropen.com)
The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. (asm.org)
P22 has strong 16S rRNA gene sequence similarity to Paenibacillus humicus (99.5%) ( 7 ). (asm.org)

2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription. (insdc.org)
NTP is the building block of DNA and RNA, a nucleotide chain produced through the DNA replication and transcription process. (zdfsbw.com)
Several transcription regulatory sequences were identified in the promoter region. (elsevierpure.com)
Primer extension experiments demonstrated the existence of two possible transcription initiation sites at nucleotide -29 and 32 position, 5' to the start of the translation. (elsevierpure.com)
In addition to a TATA box at position -29 relative to the transcription initiation site and two Spl GGGCGG recognition sequences at nucleotide positions -42 to -37 and -50 to -45, the promoter contains a sequence motif matching the transcription activating factor AP-1. (elsevierpure.com)

Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
2006. Sequencing for quasispecies analysis was done using the method described by Ramachandran et al. (cdc.gov)
0 denotes a consensus sequence with no quasispecies analysis. (cdc.gov)
CDC used whole genome sequencing (WGS) analysis to link one case to contaminated opened powdered formula from the patient's home and the other to contaminated breast pump equipment. (medscape.com)
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. (bvsalud.org)
Techniques of nucleotide sequence analysis that increase the scale of operations enabling an increase in the depth of coverage (number of copies) to which each polynucleotide is sequenced. (bvsalud.org)

Detecting the patterns of DNA sequence variants across the human genome is a crucial step for unraveling the genetic basis of complex human diseases. (psu.edu)
In this article, we present a generalized linear model for identifying specific nucleotide variants that encode complex human diseases. (psu.edu)

In biology, a substitution model , also called models of DNA sequence evolution , are Markov models that describe changes over evolutionary time. (wikipedia.org)
Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. (wikipedia.org)
Estimates of evolutionary distances (numbers of substitutions that have occurred since a pair of sequences diverged from a common ancestor) are typically calculated using substitution models (evolutionary distances are used input for distance methods such as neighbor joining ). (wikipedia.org)
[2] Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree. (wikipedia.org)
Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. (wikipedia.org)
It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). (wikipedia.org)
Most of the work on substitution models has focused on DNA/ RNA and protein sequence evolution. (wikipedia.org)
In fact, substitution models can be developed for any biological characters that can be encoded using a specific alphabet (e.g., amino acid sequences combined with information about the conformation of those amino acids in three-dimensional protein structures [7] [8] ). (wikipedia.org)
The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). (wikipedia.org)
is a type of substitution in which the nucleotide change results in the replacement of one protein building block (amino acid) with another in the protein made from the gene. (medlineplus.gov)

To export the ortholog groups into protein sequence files (in Fasta format), a protein database of all input genomes must be provided. (readthedocs.io)
A protein database file is simply a Fasta file that contains all sequences used during the ortholog search procedure, with simplified headers. (readthedocs.io)

Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). (scienceopen.com)

Nucleotide clusters in deoxyribonucleic acids. (wikidata.org)

Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution. (scienceopen.com)
The K a /K s ratio can be used to examine the action of natural selection on protein-coding regions, [5] [6] it provides information about the relative rates of nucleotide substitutions that change amino acids (non-synonymous substitutions) to those that do not change the encoded amino acid (synonymous substitutions). (wikipedia.org)

An inversion changes more than one nucleotide in a gene by replacing the original sequence with the same sequence in reverse order. (medlineplus.gov)

The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)

Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. (asm.org)

Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described. (nih.gov)
BLAST 2 Sequences' utilizes the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison. (nih.gov)
Then use the BLAST button at the bottom of the page to align your sequences. (nih.gov)
Subject sequence(s) to be used for a BLAST search should be pasted in the text area. (nih.gov)

Correlation between a coat protein amino-terminal sequence and a ribosome-binding DNA sequence from phiX 174. (wikidata.org)

We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. (plos.org)
We have determined the nucleotide sequence of a 2375-base-pair DNA fragment, which contained the sporulation gene spo0A cloned from Bacillus subtilis. (elsevierpure.com)

HCV sequence contigs were aligned and edited by hand using DNAstar to construct the final sequence for each isolate. (cdc.gov)

To address this question, we performed paired whole exome sequencing of donor and recipient DNA and single cell RNA sequencing (scRNA-seq) of 5 human kidney transplant biopsy cores. (biorxiv.org)
Exome sequences were used to define single nucleotide variations (SNV) across all samples. (biorxiv.org)
The file may contain a single sequence or a list of sequences. (nih.gov)
Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA seq. (erhard-lab.de)
Sequence-specific, single primer amplification and detection of PCR products for identification of hepatitis viruses. (cdc.gov)
We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. (asm.org)

New and updated data on nucleotide sequences contributed by research teams to each of the three databases are synchronized on a daily basis through continuous interaction between the staff at each the collaborating organizations. (wikipedia.org)
Bioinformatics Biological database List of biological databases National Center for Biotechnology Information Sequence database Karsch-Mizrachi, I. (wikipedia.org)

For sequence submission to DDBJ, it is required for submitters to provide not only nucleotide sequence but also address of submitters and contact person , reference(s) (including primary citation ), names of source organisms, function, natures of genes, and so on (collectively means " registration information " of the entry). (nig.ac.jp)
Kudoh, J, Ikeuchi, T & Kurahashi, K 1985, ' Nucleotide sequences of the sporulation gene spo0A and its mutant genes of Bacillus subtilis ', Proceedings of the National Academy of Sciences of the United States of America , vol. 82, no. 9, pp. 2665-2668. (elsevierpure.com)

Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. (scienceopen.com)

Application of the 454 GS FLX Titanium sequencing technology and sequencing of an 8-kb paired-end library resulted in 561,213 reads and 61,143,112 nucleotides. (asm.org)

Then, go through the Differential expression or the Kinetic modeling vignette, which provide a comprehensive walk-through of the two main settings of nucleotide conversion experiments. (erhard-lab.de)

BLASTN programs search nucleotide subjects using a nucleotide query. (nih.gov)
The search will be restricted to the sequences in the database that correspond to your subset. (nih.gov)
This tutorial demonstrates how to export ortholog groups from a previous Orthology search operation as protein and nucleotide sequences. (readthedocs.io)

a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (insdc.org)

The Committee concluded that additional work may be needed to assess the viability of the stocks held in VECTOR, and that further molecular characterization of additional strains may be valuable in helping to identify strains from which further DNA sequences could be determined. (who.int)

Row vector of integers from Mapping Nucleotide Integers to Letter Codes . (mathworks.com)
Character vector or string containing codes specifying a nucleotide sequence. (mathworks.cn)
Row vector of integers specifying a nucleotide sequence. (mathworks.cn)

Finds sub-sequences or patterns in the sequence and highlights the matching regions. (nih.gov)
Some regions of DNA contain short sequences of nucleotides that are repeated a number of times in a row. (medlineplus.gov)

5′−AUGGCAAGAAAA−3′ Express the sequence of amino acids using the three-letter abbreviations separated by hyphens (e.g. (answersmcq.com)
occurs when there is an addition or loss of nucleotides that shifts the grouping and changes the code for all downstream amino acids. (medlineplus.gov)

Here, we report a novel in vivo metabolic RNA sequencing method, SLAM-ITseq, which metabolically labels RNA with 4-thiouracil in a specific cell type in vivo followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion. (nih.gov)

Anatomy7

Organisms35

Diseases2

Chemicals and Drugs100

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Phenomena and Processes96

Technology, Industry, Agriculture2

Information Science7

Health Care2

Geographicals1

International Nucleotide Se2

MRNA5

European Nucleotide Archive3

Genomic2

Isolates8

Primers2

NCBI3

Guanine1

INSDC3

Codons2

Protein sequences3

Bases4

Variation1

Differentiation1

Localization1

Synthesis1

Determination3

Transcript1

Homology1

Deletions1

RRNA5

Transcription5

Analysis7

Variants2

Substitution10

FASTA2

Estimate evolutionary distances1

Clusters1

Synonymous substitutions2

Reverse1

Determine1

Genome Sequence1

BLAST5

Ribosome1

Fragment2

Isolate1

Single6

Databases2

Genes2

Differences1

Reads1

Experiments1

Search3

Promoter1

Strains1

Vector3

Regions2

Amino acids2

Specific1