Tag: GenBank

“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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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;…

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,…

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…

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…

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…

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…

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? 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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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],…

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…

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)…

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…

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…

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 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…

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…

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? 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…

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…

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…

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…

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….

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]…

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…

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…

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,…

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,…

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)….

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;…

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…

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…

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…

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…

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? 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…

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…

(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…

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…

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…

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…

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…

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…

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…

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….

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…

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…

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…

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…

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…

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…

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 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…

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…

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…

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…

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 (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…

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 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:…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…