Tag: GenBank
Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera)
“I have just been thinking, and I have come to a very important decision. These are the wrong sort of bees.”—Winnie the Pooh. A mitogenomic phylogeography of species of Apis and subspecies of Apis mellifera The mitogenomic analysis confirms with high confidence previous inferences as to morpho-behavioral relationships among nine…
read.GenBank function – RDocumentation
The function uses the site www.ncbi.nlm.nih.gov/ from where the sequences are retrieved. If species.names = TRUE, the returned list has an attribute “species” containing the names of the species taken from the field “ORGANISM” in GenBank. Since ape 3.6, this function retrieves the sequences in FASTA format: this is more…
Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness
Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…
KEGG T00166: LIC_12265
Entry LIC_12265 CDS T00166 Name (GenBank) conserved hypothetical protein KO K21472 peptidoglycan LD-endopeptidase LytH [EC:3.4.-.-] Organism lic Leptospira interrogans serovar Copenhageni Brite KEGG Orthology (KO) [BR:lic00001] 09180 Brite Hierarchies 09181 Protein families: metabolism 01002 Peptidases and inhibitors [BR:lic01002] LIC_12265 01011 Peptidoglycan biosynthesis and degradation proteins [BR:lic01011] LIC_12265Enzymes [BR:lic01000] 3. Hydrolases 3.4 Acting on peptide bonds (peptidases) 3.4.- 3.4.-.- LIC_12265Peptidases and inhibitors [BR:lic01002] Metallo peptidases Family M23 LIC_12265Peptidoglycan biosynthesis…
Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR
Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…
Class B1 GPCR activation by an intracellular agonist
Expression and purification of human PTH1R The plasmid encoding human PTH1R (GenBank identifier: U17418.1; residues 27–491) was constructed and purified as previously reported17. The construct was expressed in HEK293 GnTI (N-acetylglucosaminyltransferase I-negative) cells (American Type Culture Collection, CRL-3022) using the BacMam system (Thermo Fisher Scientific), and the cells were grown…
Genomic characteristics of ESBL-producing E. coli in China
Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…
KEGG T00661: FMG_0425
Entry FMG_0425 CDS T00661 Name (GenBank) glycine reductase complex selenoprotein KO K21577 glycine/sarcosine/betaine reductase complex component C subunit beta [EC:1.21.4.2 1.21.4.3 1.21.4.4] Organism fma Finegoldia magna Brite KEGG Orthology (KO) [BR:fma00001] 09190 Not Included in Pathway or Brite 09191 Unclassified: metabolism 99980 Enzymes with EC numbers FMG_0425Enzymes [BR:fma01000] 1. Oxidoreductases 1.21 Catalysing the reaction X-H + Y-H = X-Y 1.21.4 With a…
KEGG T07081: G7082_08800
Entry G7082_08800 CDS T07081 Name (GenBank) glycine reductase KO K21577 glycine/sarcosine/betaine reductase complex component C subunit beta [EC:1.21.4.2 1.21.4.3 1.21.4.4] Organism vhy Vagococcus hydrophili Brite KEGG Orthology (KO) [BR:vhy00001] 09190 Not Included in Pathway or Brite 09191 Unclassified: metabolism 99980 Enzymes with EC numbers G7082_08800Enzymes [BR:vhy01000] 1. Oxidoreductases 1.21 Catalysing the reaction X-H + Y-H = X-Y 1.21.4 With a disulfide as…
Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach
The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of…
LOINC 87396-8 GenBank accession number
Term Description The unique identifier assigned to an organism-specific genetic sequence submitted to a reference database such as GenBank (www.ncbi.nlm.nih.gov/genbank/). GenBank identifiers are called Accession numbers, and GenBank includes sequence data for a variety of organisms, including humans, other animals, plants, and microorganisms. Source: Regenstrief LOINC Fully-Specified Name Component GenBank…
Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data
Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…
Gap-free genome assembly of anadromous Coilia nasus
Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS Google Scholar Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…
A Guide to DNA Sequencers
DNA sequencing is a method that determines the order of the four nucleotide bases, namely, adenine (A), thymine (T), guanine (G), and cytosine (C), that form a DNA molecule. In this article, AZoLifeSciences offers a comprehensive guide to DNA Sequencers. Image Credit: Blue Andy/Shutterstock.com In a DNA double helix, nucleotide bases…
A Short History of Virology
This article is pulled from the 15 day Troubles Away program of short videos and games designed to remove troubles from your life. Considering recent global events does a short history of virology support the central insight of Troubles Away, namely that troubles appear when we believe in something that…
Characterization of nuclear DNA diversity in an individual Leymus chinensis
Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…
Solved You decide the best place to start would be the
You decide the best place to start would be the “Gene” database of the National Center for Biotechnology Information, also known as “GenBank”. You go to GenBank, select “Gene” from the database dropdown menu and input “SBE1” into the search function. a) How many results come up? The top two…
Accidental DNA collection by air sensors could revolutionize wildlife tracking
An air-quality monitoring station in London is located near a deer park, so it picks up DNA from species such as Dama dama (fallow deer) in its filters.Credit: Robert Knell Scientists might be able to keep tabs on the world’s flora and fauna by analysing DNA floating through the air….
Perl. How to retrieve data until a keyword in GenBank?
Perl. How to retrieve data until a keyword in GenBank? 0 Hello! I’m trying to write a script that retrieves data from GenBank files. I need only the info until the COMMENT part of the annotation. This is my INPUT: LOCUS mitochondrion_genome 19524 bp DNA HTG 17-DEC-2022 DEFINITION Drosophila melanogaster…
Genomic characteristics of a multidrug-resistant E. coli
Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…
Characterization of metagenome-assembled genomes from the International Space Station | Microbiome
Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…
LOC127888533 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 [Homo sapiens (human)] – Gene
NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…
Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea
Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…
KEGG T01170: Kvar_3615
Entry Kvar_3615 CDS T01170 Name (GenBank) galactose-1-phosphate uridylyltransferase KO K00965 UDPglucose–hexose-1-phosphate uridylyltransferase [EC:2.7.7.12] Organism kva Klebsiella variicola At-22 Pathway kva00052 Galactose metabolism kva00520 Amino sugar and nucleotide sugar metabolism kva01100 Metabolic pathways kva01250 Biosynthesis of nucleotide sugars Module kva_M00554 Nucleotide sugar biosynthesis, galactose => UDP-galactose kva_M00632 Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P…
Why aren’t authors specific about patch version?
I am finding difficulty finding the exact assembly version (e.g. patch version) of GRCh38 used for major databases. For instance, gnomad says “GRCh38”. But the only information on the version, for v3.1 comes from here, which says it “uses an updated version of Variant Effect Predictor (VEP) based on the…
Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)
Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…
Answered: What is GenBank ?
1 A Perspective On Human Genetics2 Cells And Cell Division3 Transmission Of Genes From Generation To Generation4 Pedigree Analysis In Human Genetics5 The Inheritance Of Complex Traits6 Cytogenetics: Karyotypes And Chromosome Aberrations7 Development And Sex Determination8 The Structure, Replication, And Chromosomal Organization Of Dna9 Gene Expression And Gene Regulation10 From…
What Are The Most Common Stupid Mistakes In Bioinformatics?
Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…
KEGG T04088: AOZ06_32105
Entry AOZ06_32105 CDS T04088 Name (GenBank) hypothetical protein KO K05553 minimal PKS acyl carrier protein Organism kphy Kibdelosporangium phytohabitans Pathway kphy01056 Biosynthesis of type II polyketide backbone kphy01100 Metabolic pathways kphy01110 Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:kphy00001] 09100 Metabolism 09109 Metabolism of terpenoids and polyketides 01056 Biosynthesis of type II polyketide backbone AOZ06_32105 00253 Tetracycline…
EMDB < EMD-17118
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
biopython – Why does my for loop in Python never stop running?
I am creating a code that takes accession numbers from an existing excel file and ultimately running it through BLAST using Entrez. I am very new to Python and pretty much just learning as a I write. Here is what my code looks like right now, it currently will run…
ZNF330/NOA36 interacts with HSPA1 and HSPA8 and modulates cell cycle and proliferation in response to heat shock in HEK293 cells | Biology Direct
Cell lines, culture conditions, heat shock treatment and transfections HeLa, HEK293 and 2D12 (a NOA36-knockout HEK293-cell line generated in this work) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a CO2 incubator. For heat…
EMDB < EMD-10691
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology
Statement on ethical considerations All animal work was approved and permitted by the Local Ethical Committee on Animal Experiments and conducted according to the Guidelines for Animal Experimentation recommendations (ARRIVE guidelines). In particular, mouse work related to C57BL/6NCrl mice was approved and permitted by the Institute of Molecular Genetics of…
Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs
Recombinant ASFVs with mosaic genomes of genotype I and II viruses detected from field samples in China During our surveillance in China, we isolated three ASFVs from pig samples collected in Jiangsu province, Henan province, and Inner Mongolia Autonomous Region, respectively, and designated them Pig/Jiangsu/LG/2021 (JS/LG/21), Pig/Henan/123014/2022 (HeN/123014/22), and Pig/Inner…
Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?
I’m a complete beginner at Perl and don’t have the slightest idea on how to do this task. I feel completely defeated. The script I’m supposed to make has to: Work with any GenBank file provided (.dat). Analyze a given interval of nucleotides in a GenBank file (specified as ARGV[0],…
Solved 0 out of 7.5 points suitable for Match the
Transcribed image text: 0 out of 7.5 points suitable for Match the followings: BLAST The Entrez Protein online database examples PubChem’s BioAssay database GenBank A. It takes the query sequence from the user and search against entire NCBI databases for similarity and then posts the output back to the person’s…
Efficient site-specific integration in CHO-K1 cells using CRISPR/Cas9-modified donors
Vector construction The Cas9/sgRNA vector (all-in-one) (GenBank accession no. OQ579018) contained sgRNA and Cas9-2A-mCherry expression cassettes. The sgRNA (5′-ATGCAGAACTAGAGTACAGC-3′) targets the phiC31 pseudo-attP intergenic site located on chromosome 3 of CHO-K1 genome (GenBank accession no. APMK01032147.1) (Fig. 1a). To construct the Cas9-mSA/sgRNA vector (GenBank accession no. OQ579019), the monomeric streptavidin (mSA)…
Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants
1. Introduction Tuberculosis (TB) is a significant global burden and is widely reported to be a major public health and economic problem, costing the world $617 billion between 2000 and 2015 and projected to cost $1 trillion between 2015 and 2030 (1). It is the second leading cause of death…
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives
Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…
Evolution and biogeography of apple stem grooving virus | Virology Journal
New Iranian isolates ASGV was detected in 18 (10.3%) of samples in both west and north west Iran (Table S1). All nine full-CP sequences contained open reading frames (ORFs) 714 nt in length with 237 deduced amino acid residues. ASGV has the codon UAG as stop codon in all sequences….
Import or read Snapgene .dna files into R
Import or read Snapgene .dna files into R 0 Hello, I was wondering if there is any package that allows reading Snapgene .dna files directly into R. Even if it does not conserve the features/primers/annotations it would be enough. I know I can export them from Snapgene into fasta or…
Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies
As of October 2021, two years since the start of the pandemic, coronavirus disease 2019 (COVID-19)-related deaths have surpassed 4,800,000 worldwide and 700,000 in the United States. Due to the severity of the pandemic combined with the advent of sequencing technologies, the amount of sequencing data within such a short…
LOC127271744 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226270255-226271122 [Homo sapiens (human)] – Gene
NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…
How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank?
How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank? 1 Dear Biostars community, I had a question regarding the BankIt (Genbank) submission for circularized genomes. Let’s say I have a circularized genome from 1 to 100000 bp. And I also…
VCL shRNA Plasmid Mouse) – Gentaur.com
Catalog number MBS8273409 Price Please ask Size 0,15 mg Other size please contact us to order other different size Test Mouse or mice from the Mus musculus species are used for production of mouse monoclonal antibodies or mabs and as research model for humans in your lab. Mouse are mature after 40…
MCQ on Nucleotide Databases – Biology MCQ
Nucleotide databases are repositories that store and provide access to nucleotide sequence data. These databases contain a vast collection of DNA and RNA sequences from various organisms, including viruses, bacteria, plants, animals, and humans. Nucleotide databases play a crucial role in genomics, molecular biology, and bioinformatics research by providing a…
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Cutler, E. B. The Sipuncula: Their Systematics, Biology, And Evolution (New York: Cornell University Press, doi.org/10.7591/9781501723643, 1994) Nielsen, C. Some aspects of spiralian development. Acta Zool. 91, 20–28, doi.org/10.1111/j.1463-6395.2009.00421.x (2010). Article Google Scholar Huang, D. Y., Chen, J. Y., Vannier, J. & Saiz Salinas, J. I. Early Cambrian sipunculan worms…
A review on blockchain for DNA sequence: security issues, application in DNA classification, challenges and future trends
Abadi M, Agarwal A, Barham P, et al. 2016 TensorFlow: large-scale machine learning on heterogeneous distributedsystems. Cornell University Library website. arxiv.org/abs/1603.04467. Published 2016. Accessed October 2016. Afshar P, Mohammadi A, Plataniotis KN. (2018) Brain tumor type classification via capsule networks, in Proc. 25th IEEE Int Conf Image Process. pp. 3129–3133….
E. coli & K. pneumoniae strains produce NDM-5 & OXA-181
1Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China; 2Department of Clinical Laboratory, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China Correspondence: Qian Chen, Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China, Tel +8618951768213, Email [email protected]…
GenBank Overview
2 hours ago Article URL: www.ncbi.nlm.nih.gov/genbank/ Comments URL: news.ycombinator.com/item?id=36038722 Points: 1 # Comments: 0 GenBank OverviewWhat is GenBank?GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which…
pMC CMV GFP T2A Puro H1 Scramble shRNA scramble control pare
Catalog number MNSI000A-1 Price Please ask Size 10 ug Shipping Temperature Blue Ice/ Dry Ice Product category Minicircle Technology Description Isotype or positive controls by peptides, antibodies and deactivated samples. Kit Plasmid mini made and maxi DNA purification kits can be silica gel or anion exchange, endotoxin free and are…
Sample GenBank Record / Visual abstracts made easy with Mind the Graph
This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can check the corresponding alive record for U49845, and seeexamples of other records the show a range of biological features. SITE SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene,…
A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus
Generally, there are two major groups of viruses that circulate in hematophagous arthropods: arthropod-borne virus (arbovirus) and arthropod-specific virus (ASV) (or arthropod-only virus). These viruses are diverse in taxonomy and may have unsegmented or segmented (two to twelve) genomes. Arbovirus are transmitted by hematophagous arthropods such as mosquitoes, ticks, sandflies,…
Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis
Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….
Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR
Introduction Microalgae encompass a large number of organisms with both prokaryotic and eukaryotic nature, making them an archetypal platform for recombinant technology (Malla et al., 2021). The nutraceutical significance of microalgae is characterized by their rich natural biomolecules and high amount of protein, vitamins, and lipid substances (Potvin and Zhang, 2010;…
Statement on the antigen composition of COVID-19 vaccines
The WHO Technical Advisory Group on COVID-19 Vaccine Composition (TAG-CO-VAC) continues to meet regularly to assess the implications of SARS-CoV-2 evolution for COVID-19 vaccine antigen composition and advise WHO on whether changes are needed to the antigen composition of future COVID-19 vaccines. In April 2023, the TAG-CO-VAC indicated that the…
Genomic and phylogenetic analysis of Klebsiella michiganens
Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…
Microorganisms | Free Full-Text | 16S-23S rRNA Internal Transcribed Spacer Region (ITS) Sequencing: A Potential Molecular Diagnostic Tool for Differentiating Lactococcus garvieae and Lactococcus petauri
1. Introduction Lactococcosis is a serious septicemic fish disease in Mediterranean countries. Lactococcus garvieae was considered the sole causative agent of lactococcosis until recently. L. garvieae has been isolated as a causative agent of the disease in several freshwater and marine species such as rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis…
Candidemia case caused by a drug-resistant Candida auris
Introduction Candida auris is a human fungal pathogen, first isolated in Japan in 2009.1 Since then, many C. auris isolates have been reported worldwide.2–4 This pathogen can contaminate the environment around the patients who were colonized by the fungus, and can survive for long periods in major outbreaks.5 Recent studies…
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Wastewater sample collection, RNA extraction, and sequencing Houston Water collected and provided weekly 24-hour time-weighted composite influent (raw wastewater) samples from 39 wastewater treatment plants (WWTPs) in Houston covering a service area of approximately 580 miles2 and serving over 2.3 million people. In total, 2637 samples were analyzed. Untreated wastewater…
Where to upload and store annotated genetic variant data online?
Where to upload and store annotated genetic variant data online? 0 Hi. I’m willing to upload my annotated genomic variant (somatic mutation) data of four bladder cancer patients sequenced by whole-exome sequencing. I have annotated them using Annovar. I have the data as excel files and also have the corresponding…
How to get the gene ID
There is a brute force method for this. You could upload the fasta sequence in tblastn and keep a filter of 100% sequence cover and blast. Usually the first hit should give you the Genbank/Refsec ID for your protein sequence. The next one will require some scripting, but if you…
Free-floating eDNA identifies presence and abundance of ocean life
(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.) (THE CONVERSATION) Ocean life is largely hidden from view. Monitoring what lives where is costly – typically requiring big boats, big nets, skilled personnel and plenty of time. An emerging technology using what’s called…
Where Can I Find Large Datasets Open to the Public?
Share Tweet Share Share Email Where Can I Find Large Datasets Open to the Public? Looking for a large dataset open to the public? We’ve gathered 15 recommendations from professionals like Administrative Managers, CEOs, and Directors. From discovering datasets on Datahub.io to accessing…
SEA-PHAGES | GenBank Submissions
Hello, I am at one of the schools that not only sends phage genomes to PITT for submission, but occassionally submits to GenBank directly when we work on different species. We do so by emailing the submission file in right from DNAM with the appropriate information. Recently I received a…
Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli
1. Introduction Shiga toxin-producing Escherichia coli (STEC) are important zoonotic pathogens comprising more than 400 serotypes (Beutin and Fach, 2015). Pathogenic STEC strains such as enterohemorrhagic E. coli (EHEC) may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. However, it remains difficult to fully define human pathogenic STEC…
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
Ethics statement All experiments with hamsters were performed in accordance with the Science Council of Japan’s Guidelines for the Proper Conduct of Animal Experiments. The protocols were approved by the Institutional Animal Care and Use Committee of National University Corporation Hokkaido University (approval ID: 20-0123 and 20-0060). All protocols involving…
Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect DNA barcodes from Colombia.
Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by…
Mosquito densovirus significantly reduces the vector susceptibility to dengue virus serotype 2 in Aedes albopictus mosquitoes (Diptera: Culicidae) | Infectious Diseases of Poverty
Identification of MDV presence using open access sequencing data Metagenomic next-generation sequencing (NGS) data for field mosquitoes in China were searched from the NCBI SRA database (www.ncbi.nlm.nih.gov/sra) and CNGB Sequence Archive database (db.cngb.org/cnsa/) using the keywords “mosquito OR Anopheles OR Aedes OR Culex”. Followed by removing the datasets with less…
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Figure 1 shows the detailed workflow of the study. Fig. 1 General overview of the study. Briefly, MPXV was isolated from a skin lesion and then was used to infect CV-1 cells. After the designated infection times, total RNA was isolated and sequenced using direct cDNA sequencing protocol on ONT’s MinION platform….
Proksee – FAQs
FAQs Below are are some common problems for users of Proksee. If your problem is not here please contact us with the details of your issue: I get errors when submitting a GenBank file for a new project. The GenBank file is probably not formatted correctly. Try using GB2sequin to…
After collecting many more gene homologous sequences
Transcribed image text: After collecting many more gene homologous sequences from GenBank, you design the following PCR primers to amplify a portion of this gene. The primers you settle on are: Forward primer: 5′-TTACTAATCACGGGATTGCAA-3′ Reverse primer: 5 – ECACACACAETAAAG C. (5 points) How long (in basepairs) will the resulting PCR…
Microorganisms | Free Full-Text | Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L
In this article, we present a description of the genome sequencing data and the draft genome of L. plantarum FCa3L. Genome sequencing was performed using the Illumina MiSeq platform and a total of 40 Mb raw data was obtained. The genome sequence of L. plantarum FCa3L at 30× coverage was…
Fgfr2 Gene trapped Allele Detail MGI Mouse (MGI:4336376)
Fgfr2Gt(G019D03)WrstGene trapped Allele Detail Symbol: Fgfr2Gt(G019D03)Wrst Name: fibroblast growth factor receptor 2; gene trap G019D03, German Gene Trap Consortium MGI ID: MGI:4336376 Gene: Fgfr2 Location: Chr7:129764181-129868538 bp, – strand Genetic Position: Chr7, 73.19 cM Mutant Cell Line: G019D03 Germline Transmission: Unknown Parent Cell Line: TBV2 (ES Cell) Strain of Origin: 129S2/SvPas Allele…
Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)
Camera surveillance and spatial analyses Camera surveillance took place between August and December 2020, at twelve ~ 30 km2 sites located in the central and northern Golan Heights (Supplementary Table 1). The sampling sites designated for this study belonged to four different land-use categories: “high culling risk”, “low culling risk”, nature reserves…
Hybrids of RNA viruses and viroid-like elements replicate in fungi
Ribozyme search of the Sequence Read Archive Observing that ribozymes are sufficiently short to be captured on a short sequence read (less than 100 nt), we reasoned it will be possible to screen large volumes of sequencing data to identify libraries potentially containing ribozyme agents. To this end we adapted…
can the controversial COVID genome database survive?
During the COVID-19 pandemic, one online platform emerged as the main repository for viral genome data. GISAID, an initiative launched in 2008 to improve the global sharing of influenza data, earned the trust of scientists by ensuring that they would be credited for the data they generated. It now hosts…
Best way to obtain info from genbank given accession codes
Best way to obtain info from genbank given accession codes 1 Hi all, I have a lot of (order of a million) accession codes that I need to fetch info of from genbank. I have found these by blasting nucleotide sequences against the nt database. I’d like to know whether…
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
scEC&T sequencing A detailed, step-by-step protocol of scEC&T-seq is available on the Nature Protocol Exchange46 and is described below. The duration of the protocol is approximately 8 days per 96-well plate. Cell culture Human tumor cell lines were obtained from ATCC (CHP-212) or were provided by J. J. Molenaar (TR14; Princess…
4. A GenBank-formatted DNA sequence file is presented
Transcribed image text: 4. A GenBank-formatted DNA sequence file is presented below. Assume that this sequence represents the sense strand, starts with the 5’UTR, contains two exons, has a single intron, and ends with the 3 ‘UTR. The protein coding sequences have the following coordinates: 343..561,760..1353 (indicated at the CDS…
EMDB < EMD-16884
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
E&C Republicans Seek Data and Documents from NIH on Early COVID Cases
Committee seeks to improve pandemic preparedness, strengthen grant oversight, and enhance the biosafety of lab and field research Washington, D.C. — House Energy and Commerce Committee Chair Cathy McMorris Rodgers (R-WA), Subcommittee on Oversight and Investigations Chair Morgan Griffith (R-VA), and Subcommittee on Health Chair Brett Guthrie (R-KY) today on…
GenBank Release 255.0 is Available!
GenBank release 255.0 (4/21/2023) is now available on the NCBI FTP site. This release has 23.44 trillion bases and 3.48 billion records. During the 58 days between the close dates for GenBank Releases 254.0 and 255.0, the traditional portion of GenBank grew by 95,444,070,395 base pairs and by 724,301 sequence…
Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes | BMC Genomics
Laboratory methods Tissue samples of lizards were collected over the course of several field seasons in Indonesia under appropriate permits as part of a biotic survey of mountains across the island of Sulawesi. Liver tissues were dissected and stored in RNA-later, which were incubated at ambient temperature for 24 to…
rRNA contaminants RNASeq
rRNA contaminants RNASeq 0 Hi, I’m currently trying to find out if my the level of rRNA contamination in my RNASeq samples. I saw this was mentioned before: aligning the samples to rRNA sequences from Genbank using bowtie2 would show me an estimate, but I just wanted to be sure:…
EMDB < EMD-29544
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Evidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34
Three samples of S. 4,[5],12:i:-, all isolated in 2010, harbored mcr-3.1. Two were from human stool and the other was from ready-to-eat frozen food. Phenotypic characterization confirmed that all three isolates were resistant to colistin, all with MIC and MBC of 8 µg/ml. WGS of H1-012, H1-014 and H1-120 were analyzed…
Coming Soon! Including Sample Location and Collection Date and Time for Sequences Submitted to GenBank and SRA – NCBI Insights
As previously announced, in collaboration with our partners at the International Nucleotide Sequence Database Collaboration (INSDC), we will begin to systematically gather ‘location of collection’ and ‘date and time of collection’ for sequence data submitted to GenBank and the Sequence Read Archive (SRA). Gathering information about where and when a…
KEGG T07380: KHQ08_13675
Entry KHQ08_13675 CDS T07380 Name (GenBank) sarcosine oxidase subunit alpha KO K00302 sarcosine oxidase, subunit alpha [EC:1.5.3.24 1.5.3.1] Organism pscq Pseudochrobactrum algeriensis Pathway pscq00260 Glycine, serine and threonine metabolism pscq01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:pscq00001] 09100 Metabolism 09105 Amino acid metabolism 00260 Glycine, serine and threonine metabolism KHQ08_13675Enzymes [BR:pscq01000] 1. Oxidoreductases 1.5 Acting on the CH-NH group of…
KEGG T04391: AYI71_03445
Entry AYI71_14940 CDS T04391 Name (GenBank) cysteine desulfurase NifS KO K04487 cysteine desulfurase [EC:2.8.1.7] Organism lor Limosilactobacillus oris Pathway lor00730 Thiamine metabolism lor01100 Metabolic pathways lor01240 Biosynthesis of cofactors lor04122 Sulfur relay system Brite KEGG Orthology (KO) [BR:lor00001] 09100 Metabolism 09108 Metabolism of cofactors and vitamins 00730 Thiamine metabolism AYI71_14940 09120 Genetic Information Processing 09123 Folding, sorting and degradation 04122…
KEGG T04758: B5M06_02655
Entry B5M06_03110 CDS T04758 Name (GenBank) dihydroorotase KO K01465 dihydroorotase [EC:3.5.2.3] Organism cke Comamonas kerstersii Pathway cke00240 Pyrimidine metabolism cke01100 Metabolic pathways cke01240 Biosynthesis of cofactors Brite KEGG Orthology (KO) [BR:cke00001] 09100 Metabolism 09104 Nucleotide metabolism 00240 Pyrimidine metabolism B5M06_03110Enzymes [BR:cke01000] 3. Hydrolases 3.5 Acting on carbon-nitrogen bonds, other than peptide bonds 3.5.2 In cyclic amides 3.5.2.3 dihydroorotase B5M06_03110 BRITE hierarchyBRITE hierarchy SSDB OrthologParalogGene clusterGFIT…
KEGG T03355: LACWKB8_1696
Entry LACWKB8_1696 CDS T03355 Name (GenBank) Beta-glucoside bgl operon antiterminator, BglG family KO K03488 beta-glucoside operon transcriptional antiterminator Organism law Lactobacillus sp. wkB8 Brite KEGG Orthology (KO) [BR:law00001] 09180 Brite Hierarchies 09182 Protein families: genetic information processing 03000 Transcription factors [BR:law03000] LACWKB8_1696Transcription factors [BR:law03000] Prokaryotic type Other transcription factors BglG family LACWKB8_1696 BRITE hierarchyBRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: PRD…
Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with master and global regulators
ANR is relatively conserved among diarrheagenic pathogens Over the last 5 years, massive sequencing of new bacterial genomes has identified hundreds of new ANR members in multiple pathogens. ANR is widely distributed in at least 26 Gram-negative bacterial species29,31. Phylogenetic analysis of the amino acid sequence of ANR members from clinically…
KEGG T00139: BP2248
Entry BP2248 CDS T00139 Symbol bscJ Name (GenBank) putative type III secretion protein KO K03222 type III secretion protein J Organism bpe Bordetella pertussis Tohama I Pathway bpe03070 Bacterial secretion system Brite KEGG Orthology (KO) [BR:bpe00001] 09130 Environmental Information Processing 09131 Membrane transport 03070 Bacterial secretion system BP2248 (bscJ) 09180 Brite Hierarchies 09183 Protein families: signaling and cellular processes 02044…
KEGG T08735: BAE_06355
Entry BAE_06355 CDS T08735 Name (GenBank) PTS lactose/cellobiose transporter subunit IIA KO K02759 cellobiose PTS system EIIA component [EC:2.7.1.196 2.7.1.205] Organism baer Bacillus aerophilus Pathway baer00500 Starch and sucrose metabolism baer02060 Phosphotransferase system (PTS) Brite KEGG Orthology (KO) [BR:baer00001] 09100 Metabolism 09101 Carbohydrate metabolism 00500 Starch and sucrose metabolism BAE_06355 09130 Environmental Information Processing 09131 Membrane transport 02060 Phosphotransferase system…
KEGG T01822: RAM_16160
Entry RAM_35150 CDS T01822 Name (GenBank) microsomal epoxide hydrolase KO K21159 epoxide hydrolase Organism amn Amycolatopsis mediterranei S699 Pathway amn01059 Biosynthesis of enediyne antibiotics Brite KEGG Orthology (KO) [BR:amn00001] 09100 Metabolism 09109 Metabolism of terpenoids and polyketides 01059 Biosynthesis of enediyne antibiotics RAM_35150 09180 Brite Hierarchies 09181 Protein families: metabolism 01008 Polyketide biosynthesis proteins [BR:amn01008] RAM_35150Polyketide biosynthesis proteins [BR:amn01008] Polyketide tailoring proteins Oxygenase RAM_35150…
KEGG T03562: M667_06130
Entry M667_06130 CDS T03562 Name (GenBank) ribonucleoside-diphosphate reductase KO K00525 ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1] Organism cbal Cellulophaga baltica NN016038 Pathway cbal00230 Purine metabolism cbal00240 Pyrimidine metabolism cbal01100 Metabolic pathways cbal01232 Nucleotide metabolism Module cbal_M00053 Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP Brite KEGG Orthology (KO) [BR:cbal00001] 09100 Metabolism 09104 Nucleotide metabolism 00230 Purine metabolism M667_06130 00240 Pyrimidine metabolism M667_06130 09180 Brite…
KEGG T07833: LAD35_14290
Entry LAD35_14290 CDS T07833 Name (GenBank) thymidylate synthase KO K00560 thymidylate synthase [EC:2.1.1.45] Organism codo Comamonas odontotermitis Pathway codo00240 Pyrimidine metabolism codo00670 One carbon pool by folate codo01100 Metabolic pathways codo01232 Nucleotide metabolism Module codo_M00938 Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP Brite KEGG Orthology (KO) [BR:codo00001] 09100 Metabolism 09104 Nucleotide metabolism 00240 Pyrimidine metabolism LAD35_14290 09108 Metabolism of…
KEGG T02677: SSYRP_v1c07610
Entry SSYRP_v1c07610 CDS T02677 Symbol coaE Name (GenBank) dephospho-CoA kinase KO K00859 dephospho-CoA kinase [EC:2.7.1.24] Organism ssyr Spiroplasma syrphidicola Pathway ssyr00770 Pantothenate and CoA biosynthesis ssyr01100 Metabolic pathways ssyr01240 Biosynthesis of cofactors Module ssyr_M00120 Coenzyme A biosynthesis, pantothenate => CoA Brite KEGG Orthology (KO) [BR:ssyr00001] 09100 Metabolism 09108 Metabolism of cofactors and vitamins 00770 Pantothenate and…