Tag: GenBank

Ants of French Guiana: 16S rRNA sequence dataset

doi: 10.3897/BDJ.11.e91577. eCollection 2023. Affiliations Expand Affiliations 1 UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French Guiana UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles) Kourou French Guiana. 2 Laboratoire Evolution et…

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A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

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Ubuntu Manpage: gt-encseq-encode – Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.

Provided by: genometools_1.6.5+ds-2_amd64 NAME gt-encseq-encode – Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently. SYNOPSIS gt encseq encode sequence_file [sequence_file [sequence_file …]] DESCRIPTION -showstats [yes|no] show compression results (default: no) -ssp [yes|no] output sequence separator positions to file (default: yes) -des [yes|no] output sequence descriptions to file (default: yes) -sds [yes|no]…

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Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species

Mitogenome organization, composition, and skewness The complete mitochondrial genome of B. dussumieri is (GenBank accession XX) 16,685 bp of length, which is similar to other mudskippers mitogenomes (16,470–17,243 bp) (Tables 1 and 2). The mitochondrial genome and the structure were also typical of the mudskipper species and with highly conservative sites, comprising…

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Georgian Wheat Culture Celebrated at International Conference

Tbilisi, Georgia: The Georgian Academy of Agricultural Sciences, the Ivane Javakhishvili State University, and the Agricultural Research Center hosted an international scientific conference on Georgian wheat culture on February 6 and 7, 2024. The conference aimed to protect and popularize Georgian wheat, a rich and diverse genetic resource and a part…

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FASTQ to FASTA Converter

About the tool The FASTA format is a text-based format for representing nucleotide or peptide sequences. The FASTQ format additionally includes the corresponding quality scores. This tool allows you to convert FASTQ files to FASTA. The resulting FASTA file will contain only the sequence data from the input FASTQ file….

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Chinese Scientist Filed Covid Sequence Weeks Before Official Release: Report

Beijing: A Chinese scientist sought to publish the genetic profile of the coronavirus two weeks before Beijing formally released the sequence, as per federal documents shared with a US congressional committee and released on Wednesday, The Washington Post reported. The delay may have slowed researchers’ work on tests, treatments, and…

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‘Chinese experts mapped Covid virus 2 weeks before officially informing world’

NEW YORK: A team of Chinese researchers identified and mapped SARS-CoV-2, the virus that caused the Covid-19 pandemic, at least two weeks before the country officially informed the world about the virus, according to media reports. The reports, based on documents from the US department of health and human services…

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Genetic Sequence of Coronavirus Was Submitted to US Database 2 Weeks Before China’s Official Disclosure, Documents Show

The genetic sequence itself doesn’t indicate the origins of the virus that causes Covid-19. (Alissa Eckert/Dan Higgins/CDC) The genetic sequence of SARS-CoV-2, the virus that causes COVID-19, was submitted to a National Institutes of Health database two weeks before its release by the Chinese regime, according to documents that were…

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Chinese Lab Sequenced COVID-19 Weeks Before Beijing Disclosed Data

Once again the timeline surrounding the COVID-19 pandemic has shifted – this time with the revelation that a researcher based in Beijing had already mapped the COVID-19 sequence two weeks before the CCP revealed its details to the world, raising questions over what other critical information China may have obscured…

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Did China really lie about Covid-19? Here’s what US says

A health worker injects a man with a shot of the Inavac vaccine for Covid-19 at the Jakarta provincial health office on Dec. 19, 2023. — AFP China most certainly acquired the first known gene sequence for Covid-19 weeks before making it public, despite Beijing’s assertion that it did so…

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Chinese scientist revealed Covid sequence weeks ahead of official release: US committee

Public health experts who examined the documents said the experience showed how there was a chance to find out more information about the virus early on in the global health emergency Image Courtesy Agencies According to federal documents provided with a US congressional committee and made public on Wednesday, a…

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Sen. Marshall Calls For Halt of Gain-of-Function Studies, Funding Chinese Research

Sen. Roger Marshall (R-Kan.) speaks on border security and Title 42 during a press conference at the U.S. Capitol in Washington on May 11, 2023. (Kevin Dietsch/Getty Images) It has been four years since patients sickened with unexplained pneumonia started appearing at hospitals in the central Chinese city of Wuhan. But…

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Chinese Scientists Shared Coronavirus Data with US Before Pandemic

In late December 2019, eight pages of genetic code were sent to computers at the National Institutes of Health in Bethesda, Md. Unbeknown to American officials at the time, the genetic map that had landed on their doorstep contained critical clues about the virus that would soon touch off a…

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Federal secrets spill on COVID origins amid rodent research on risks of lab mods, vax in pregnancy

The National Institutes of Health appears to be struggling to hide its dirty laundry on COVID-19 origins against a rash of leaks, congressional probes, and Freedom of Information Act requests, even when officials are determined to thwart sunlight. The ongoing exposure of their communications and actions isn’t the only thing…

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Chinese hospital finds new genetic sequence for rare blood type p during routine tests

It said staff at the Taixing People’s Hospital submitted the genetic sequence to the GenBank sequence database, an open access collection maintained by the National Centre for Biotechnology Information in the United States. In December, the US centre said the nucleotide sequence present in the sample had not been detected…

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Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control

Isolate characteristics From June 2020 to October 2021, our analysis included a total of 28 isolates from patient and environmental samples, all subjected to Whole Genome Sequencing (WGS) (refer to Table 1). To ensure robustness and minimize the influence of sequencing errors on our findings, all 28 WGS datasets maintained a…

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Newly discovered hedgehog species diverged from others more than a million years ago

A living Mesechinus orientalis sp. nov. (XC 2205003) from Xuancheng, Anhui. Credit: ZooKeys (2023). DOI: 10.3897/zookeys.1185.111615 Researchers at Anhui Normal University, Wuhu, China, have announced the discovery of a new species within the hedgehog genus Mesechinus. The eastern China hedgehog species was found to be distinct from other regional hedgehogs…

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Seroprevalence and Molecular Characterization of B. abortus

Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…

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KEGG T08053: IA203_01755

Entry IA203_01755       CDS       T08053                                  Name (GenBank) UDP-N-acetylmuramate dehydrogenase   KO K00075   UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98] Organism cwk  Corynebacterium wankanglinii Pathway cwk00520   Amino sugar and nucleotide sugar metabolism cwk00550   Peptidoglycan biosynthesis cwk01100   Metabolic pathways cwk01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:cwk00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    IA203_01755  09107 Glycan biosynthesis and…

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KEGG T09148: BWI76_09435

Entry BWI76_09435       CDS       T09148                                  Name (GenBank) glutaredoxin, GrxA family   KO K03674   glutaredoxin 1 Organism klm  Klebsiella sp. M5al Brite KEGG Orthology (KO) [BR:klm00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03110 Chaperones and folding catalysts [BR:klm03110]    BWI76_09435Chaperones and folding catalysts [BR:klm03110] Protein folding catalysts  Protein disulfide isomerase   BWI76_09435 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Glutaredoxin Glrx-like Thioredoxin_3…

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Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

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Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

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Analysis of sepsis combined with pulmonary infection by mNGS

Introduction Sepsis is one of the major diseases that poses a serious threat to human health, and its incidence and in-hospital mortality rates remain high despite the continuous updating of sepsis guidelines.1 Its main clinical manifestations are elevated body temperature, chills, and rapid heart rate, and it is most common…

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Preclinical assessment of an anti-HTLV-1 heterologous DNA/MVA vaccine protocol expressing a multiepitope HBZ protein | Virology Journal

Design of the recombinant virus MVA-HBZ The multiepitope protein design was based on HBZ sequence deposited in the GenBank database [17, 23, 24], and in silico analyses performed using the epitope prediction tools: NetMHCpan 4.0 (Threshold: weak binders—2.0; strong binders—0.5), NetCTL 1.2 (Threshold of 0.75) and IEDB—MHC-I Binding Predictions. Epitopes…

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Bioinformatics Unravelling the Intricate Thread of Biological Information Fabric

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, especially genetic data. With the advances in biotechnology and sequencing technologies, a huge amount of biological and genetic data is being generated each day which needs to be analyzed using computational techniques. This is where…

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Data from the development and evaluation of a CRISPR/Cas12a-based biosensor for the detection of DNA from Pseudogymnoascus destructans using samples collected from various species of bats across the United States, from 2018 to 2023

Reported here are the fluorescence data points recorded from CRISPR/Cas12a biosensor assays to detect the presence or absence of DNA from Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome in bats, from artificial controls, dermal swab, and guano samples. Ct values from qPCR experiments are also provided in…

Continue Reading Data from the development and evaluation of a CRISPR/Cas12a-based biosensor for the detection of DNA from Pseudogymnoascus destructans using samples collected from various species of bats across the United States, from 2018 to 2023

Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells

Cell lines and reagents HAP1 cells used to generate the reporter cells were grown from a frozen stock of HAP1 (C859) passage 6 purchased from Horizon Discovery LTD (Cambridge, UK). Iscove’s media (Ref: 098–150, Wisent) supplemented with 10% Fetal Bovine serum (Multicell) was used to grow HAP1 cells. All cells…

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Identification of breeding habitats and kdr mutations in Anopheles spp. in South Korea | Malaria Journal

Characteristics of potential breeding sites for Anopheles Malaria is prevalent in South Korea, with an average of 500 cases annually. COVID-19 disrupted malaria services, leading to a significant increase in cases and deaths worldwide [38]. Interestingly, the number of malaria cases in Korea decreased below 274 during the COVID-19 pandemic,…

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Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

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Table 1 | Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic

Family/genus Species mtDNA nuDNA COI (GenBank) 12S16S (GenBank) ND4 (GenBank) RAG1 (GenBank) CarcharhinidaeCarcharhinus C. acronotus (OK092567) C. acronotus (OK169912) C. acronotus (OK094394) C. acronotus (OK104478) C. falciformis (FJ519607) C. falciformis (OK169913) C. falciformis (OK094395) C. falciformis (OK104479) C. leucas (OK092568) C. leucas (OK169914) C. leucas (OK094396) C. leucas (OK104480) C….

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Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

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Update to GenBank Qualifier – NCBI Insights

‘Country’ will transition to ‘Geographic Location’ effective June 2024 As announced earlier this year, 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). As part of this effort and to make location data more accurate and informative,…

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10 You have a sequence of DNA obtained from GenBank and you are trym .docx – 10 You have a sequence of DNA obtained from GenBank and you are trym

10 You have a sequence of DNA obtained from GenBank and you are trym Sequence (nucleotide positions given on right): GCAGAGAGACTTAATGAGTACCTTATCCCCATATGGCGC ACCTTGTGGAAGAA TATAGCGACAATGGTATATGTCTAGAAGTTCGGAATATAT ATACAATATCATATGTT TTTCACATTGAAAGGGGAGGAGAATCATTAAACAACAA AAACGGCTCC TTACGCCCGATTGCTGACGCTGTTATTTGCGCTCATCTTC TTGCTGCCTCATTT CTGCAGCAGCGGCGGCAAATCTTAATGGGACGCTATGC AA (112) (160) (214) (254) (0.5 point) Which of these two is more likely to be an actual start codon for…

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Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene?

Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene? 0 Hello, I am trying to do some analysis on bacterial assemblies containing a particular AMR gene. I tried searching through NCBI genbank, refseq and it does not give me all the assemblies….

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Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…

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Which one of the following is a depiction of the GenBank sequence entry format? -triyambak.org

#Question id: 13095 #Section 7: Recombinant DNA technology and Other Tools in Biotechnology You are practicing designing primers that you can use in PCR reactions. You want your primers to allow you to amplify the sequence found below.      (a) 5’-ACTTCGATATGTCTAAAATAC-3’ and 5’- CGGTAGCGTCTCTGGTTAGCT -3’ (b) 5’-TGAAGCTATACAGATTTTATG-3’ and 5’-GCCATCGCAGAGACCAATCGA-3’…

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Long PCRSeq – Microsynth – CH

    Explore expanded possibilities with Microsynth’s Long PCRSeq, leveraging the cutting-edge long-read sequencing technology from Oxford Nanopore Technologies (ONT) to sequence clonal linear DNA ranging from 600 bp to 50 kb in length. Conveniently accessible for samples in tubes and 96-well plates, this service builds upon the capabilities of…

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Phylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China

Phylogenetic analysis of lineage IIb C.1 containing all ten local MPXV from Guangdong To rapidly characterize the phylogeny of the MPXVs involved in the outbreak in Guangdong, we constructed a phylogenetic tree by integrating 10 MPXV sequences from Guangdong into the global MPXV genetic diversity sequences derived from GISAID (Fig. 1a,…

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Foods | Free Full-Text | Isothermal Amplification and CRISPR/Cas12a-System-Based Assay for Rapid, Sensitive and Visual Detection of Staphylococcus aureus

1. Introduction Staphylococcus aureus [1], one of the top five foodborne pathogens, has a common and strong aggressiveness in humans and can secrete multiple toxic proteins (Pathogenic enterotoxins, Hemolysin, PVL) [1,2] which can cause bacteraemia, endocarditis, meningitis, toxic shock syndrome, pneumonia and other dangerous infectious diseases [3]. Moreover, the worldwide…

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Biosensors | Free Full-Text | CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus

1. Introduction Orientia tsutsugamushi (OT) is an obligate intracellular parasite bacteria and the causative agent of scrub typhus (ST), which is associated with acute febrile illness (AFI) [1] and transmitted by mites through an infected chigger bite (in the larval stage). This disease, which was earlier believed to be endemic…

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In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day

doi: 10.1111/1755-0998.13909. Online ahead of print. Affiliations Expand Affiliations 1 Microbiome Analysis Laboratory, Systems Biology Department, CNB-CSIC, Madrid, Spain. 2 Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain. 3 Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain….

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Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…

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Figure 1. Phylogenetic tree based on 16S rRNA gene sequences showing the relationship among the Restreneoebole agentea isolates and between representatives of other related taxa. The scale bar indicates 0.2 substitutions per nucleotide position. The number beside the node is the statistical bootstrap value. In brackets are the GenBank accession numbers of closest relatives. The gene sequence of Trichoderma sp. (HQ630962.1) was used as an out-group : Isolation and Identification of Bacteriocin-Producing Bacillus spp from Rastrineobola argentea (Omena) with Activity against Bovine Mastitis Bacterial Pathogens : Science and Education Publishing

Figure 1. Phylogenetic tree based on 16S rRNA gene sequences showing the relationship among the Restreneoebole agentea isolates and between representatives of other related taxa. The scale bar indicates 0.2 substitutions per nucleotide position. The number beside the node is the statistical bootstrap value. In brackets are the…

Continue Reading Figure 1. Phylogenetic tree based on 16S rRNA gene sequences showing the relationship among the Restreneoebole agentea isolates and between representatives of other related taxa. The scale bar indicates 0.2 substitutions per nucleotide position. The number beside the node is the statistical bootstrap value. In brackets are the GenBank accession numbers of closest relatives. The gene sequence of Trichoderma sp. (HQ630962.1) was used as an out-group : Isolation and Identification of Bacteriocin-Producing Bacillus spp from Rastrineobola argentea (Omena) with Activity against Bovine Mastitis Bacterial Pathogens : Science and Education Publishing

How can I obtain the DNA sequences of each CDS for several genbank files?

How can I obtain the DNA sequences of each CDS for several genbank files? 0 Hello, I want to obtain DNA sequences of all the CDS from multiple genbank files in one fasta file. I tried several solutions with Biopython but nothing is working for me. I tried for exemple…

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Metagenomic next-gene sequencing for respiratory infections

Introduction Respiratory tract infections are common and occur frequently. Rapid and accurate microbial detection is essential for timely and appropriate treatment. Traditional microbial detection methods have some limitations such as dependence on morphology, long duration, low sensitivity, and high variability.1,2 Metagenomic next-generation sequencing (mNGS) is a new detection technology characterized…

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Luteibacter jiangsuensis blood stream infection: a first case report | BMC Infectious Diseases

Gram staining, culture conditions, and antimicrobial susceptibility testing Gram staining was performed using the neo-B&M Wako (Fujifilm Wako Chemicals, Osaka, Japan). The L. jiangsuensis isolate was grown at 37 ℃ for 24 h on Sheep Blood Agar (T) (Nippon Becton Dickinson, Tokyo, Japan) and Drigalski Lactose Agar (Eiken Chemical, Tokyo, Japan)….

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Gene association analysis of an osteopontin polymorphism and ketosis resistance in dairy cattle

Methods Approval for animal experiments The prof. Dorota Ziyba-Przybylska as a Chairman of ethics review board and Dean of the Faculty of Animal Science, University Agriculture in Krakow considers that this type of project does not fall under the legislation for the protection of animals used for scientific purposes. The…

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UK releases world’s largest collection of human genome

1 of 1 DNA – Image: Freepik DNA – Image: Freepik Hey UK Biobank – Database for genetic, health and other biological data – Complete sequences released for Genome of 500,000 volunteers British. now, Researchers People around the world can request access to the data and use it to investigate…

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Inside undergraduate research with SEA-PHAGES

Molecular biology professor Vassie Ware said she’s always been interested in the dynamics of genetics. As a researcher, she’s studied genes in different systems and organisms, with early research showing that isolating viruses might be the solution to reduce the effects of medical diseases.  When she found out about Howard…

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Go to the “Gene” datsa base, and search for “delta globin” what is; the GenBank Accession Number for this gene

Now lets look at a flat file for delta globin and answer the following questions.   Go to the “Gene” data base, and search for “delta globin”. Choose the HBD link for human delta globin. Find the accession number NM_000519.3 under mRNA and protein. This will bring you to the mRNA…

Continue Reading Go to the “Gene” datsa base, and search for “delta globin” what is; the GenBank Accession Number for this gene

Borrelia puertoricensis in opossums (Didelphis marsupialis) from Colombia | Parasites & Vectors

Oppler Z, Keeffe K, McCoy K, Brisson D. Evolutionary genetics of Borrelia. Curr Issues Mol Biol. 2021;42:97–112. doi.org/10.21775/cimb.042.097.2. Article  PubMed  Google Scholar  Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: the example of the genus Borrelia. Ticks Tick Borne Dis. 2020;11:101335. doi.org/10.1016/j.ttbdis.2019.101335….

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Solved You are given a list of seven 16S rRNA gene sequences

You are given a list of seven 16S rRNA gene sequences (below) from unknown organisms. Based on the instructions below go to Genbank and identify them. Then Google or go to the original publication that describe the organism to find out what each is famous for (for example “fixes nitrogen”,…

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Index of /~psgendb/doc/local/pkg/EMBOSS/linux-x86_64/share/EMBOSS/test/genbank

Name Last modified Size Description Parent Directory   –   acnum.hit 2011-08-16 10:59 620   acnum.trg 2011-08-16 10:59 1.5K   des.hit 2011-08-16 10:59 1.6K   des.trg 2011-08-16 10:59 4.9K   division.lkp 2011-08-16 10:59 520   entrynam.idx 2011-08-16 10:59 1.0K   gbbct1.seq 2011-08-16 10:59 70K   gbest1.seq 2011-08-16 10:59 4.0K  …

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Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. Whole-genome sequence alignments link evolution at the nucleotide level across species and are a critical but computationally intensive step for…

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Which program, tool, or strategy do you use to visualize genomic rearrangements?

Which program, tool, or strategy do you use to visualize genomic rearrangements? 5 Which program, tool, or strategy do you use to visualize genomic rearrangements? In relation to my master thesis I’m working on tools to visualize fusion genes. In that regard I’m interested in any and all strategies and…

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Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…

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Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China | Virology Journal

Viral metagenomic analysis The number of clean reads was 21,157,543 for the RNA sample and 26,789,502 for the DNA sample. For RNA, the data were assembled to a total sequence length of 2,337,534, with 60.92% GC content. The length of the largest contig was 11,556 nt, which was identified as…

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Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

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DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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KEGG T00196: STH138

Entry STH138            CDS       T00196                                  Name (GenBank) putative N-acetyl-mannosamine transferase   KO K05946   N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase [EC:2.4.1.187] Organism sth  Symbiobacterium thermophilum Pathway sth00552   Teichoic acid biosynthesis Brite KEGG Orthology (KO) [BR:sth00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00552 Teichoic acid biosynthesis    STH138 09180 Brite Hierarchies  09181 Protein families: metabolism   01003 Glycosyltransferases [BR:sth01003]    STH138Enzymes [BR:sth01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.187  N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase     STH138Glycosyltransferases [BR:sth01003] Polysaccharide  Bacterial polysaccharide (excluding LPS)   STH138 BRITE hierarchy SSDB…

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Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer

A. Bioinformatics analyzes Search strategy and study selection From April to June 2021, we read relevant and related publications in Medline, EMBASE, Web of Science, and Wanfang. The search term “NOX4” have been used. The articles that fit specified criteria were all added at once: (1) Participants were split into…

Continue Reading Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer

Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

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Python function to export the annotated records to genbank file using python and biopython

Python function to export the annotated records to genbank file using python and biopython 0 def export_annotated_data(annotated_records, output_file): Convert records to genbank format SeqIO.write(annotated_records, output_file, “genbank”) it throws an error of str ‘name’ missing biopython python bioinformatic programming • 20 views • link updated 1 minute ago by barslmn ★…

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KEGG T03531: KR75_11080

Entry KR75_11080        CDS       T03531                                  Name (GenBank) xylose isomerase   KO K01805   xylose isomerase [EC:5.3.1.5] Organism kvd  Klebsiella variicola DX120E Pathway kvd00040   Pentose and glucuronate interconversions kvd00051   Fructose and mannose metabolism kvd01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:kvd00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    KR75_11080   00051 Fructose and mannose metabolism    KR75_11080Enzymes [BR:kvd01000] 5. Isomerases  5.3  Intramolecular oxidoreductases   5.3.1  Interconverting aldoses and…

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Tools for Efficient Retrieval from GEO and SRA Databases | by Denis Odinokov, MBBS, MSc, PMP | Nov, 2023

Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…

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Python Tools for Genomic Data Analysis: From Sequences to Structures | by Bao Tram Duong | Nov, 2023

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

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Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Biopython is an open-source collection of Python tools for computational biology and bioinformatics. It provides modules and classes to work with biological data such as DNA, RNA, protein sequences, structures, and more. Biopython aims to make it easy for developers to access and manipulate biological data in a programmatic way….

Continue Reading Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century

Distributed cgMLST scheme and the species tree based on a global dataset of 70,000 Neisseria genomes To set up the new dcgMLST scheme, we established a global collection of genomic sequences for 69,994 Neisseria strains (Supplementary Data 1), consisting of 4411 assembled genomes from GenBank, 65,434 genomes assembled based on short…

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CRISPR-Cas9 Gene Editing Is On The Cusp Of Something Big

Natali_Mis Gene editing, also known as genome editing, is a method where the DNA of an organism is modified using biotechnological techniques. It allows scientists to add, remove, or alter genetic material at particular locations in the genome. This 2-part series will cover the basics of CRISPR-Cas9 (see below) in…

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Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system

Construction of the VgrG database Encoded as a stand-alone gene or fused at the N-terminus of the toxin, the MIX domains can assist the delivery of their cognate T6SS effector19,20. As the central component of the spike complex, VgrG is a good marker to explore the potential conserved domains involved…

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Implications for future eDNA projects

Environmental DNA metabarcoding (eDNA) is a rapidly emerging field in which high-throughput sequencing is used to catalogue the biodiversity of ecosystems through the amplification of DNA extracted from environmental samples (water, air, faeces and soil). Although eDNA has strong links to DNA barcoding, the molecular marker most often used to…

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BLAST hits on viruses relate to different host than used

BLAST hits on viruses relate to different host than used 0 Hey guys, I have just recently (9 days ago) posted about metagenomic analysis of phages. I hope it is okay, to post again right now, the issue is different this time. I am struggling a bit with deciding which…

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Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…

Continue Reading Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA

Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand

Abstract Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using…

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KEGG T00046: PM0721

Entry PM0721            CDS       T00046                                  Symbol ttrA Name (GenBank) TtrA   KO K08357   tetrathionate reductase subunit A Organism pmu  Pasteurella multocida subsp. multocida Pm70 Pathway pmu00920   Sulfur metabolism pmu01100   Metabolic pathways pmu01120   Microbial metabolism in diverse environments pmu02020   Two-component system Brite KEGG Orthology (KO) [BR:pmu00001] 09100 Metabolism  09102 Energy metabolism   00920 Sulfur metabolism    PM0721 (ttrA) 09130 Environmental Information Processing  09132 Signal…

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EMDB < EMD-14025

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…

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National Center for Wildlife discovers new scorpion species in Riyadh

Saudi Gazette report RIYADH — A groundbreaking discovery has been made by the National Center for Wildlife (NCW), as a new species of scorpion from the Leiurus genus was identified in the Majami Al-Hadb Reserve, located in southern Riyadh. The revelation, backed by comprehensive shape and genetic analyses, has been…

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Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

Blood samples, DNA extraction, mitochondrial genome amplification and sequencing Following established procedures, bat blood samples were collected from designated sampling sites in Kanchanaburi, located in western Thailand, during the years 2019 and 202123,33,34. For this study, four bat samples (2 Myotis siligoensis and 2 Hipposideros gentilis) were utilized. These samples…

Continue Reading Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

What is NCBI GenBank? | 5 Answers from Research papers

What are the ways tourism can empower rural women in cultural preservation and representation? 5 answers How do protein modifications function in viruses? 3 answers What are the risks and benefits of each method of trigger finger release? 5 answers What are cold-water corals? 5 answers Can i apply principal…

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EMDB < EMD-16930

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…

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KEGG T00183: SAS2563

Entry SAS2563           CDS       T00183                                  Name (GenBank) putative histidinol dehydrogenase   KO K00013   histidinol dehydrogenase [EC:1.1.1.23] Organism sas  Staphylococcus aureus subsp. aureus MSSA476 (MSSA) Pathway sas00340   Histidine metabolism sas01100   Metabolic pathways sas01110   Biosynthesis of secondary metabolites sas01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:sas00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    SAS2563Enzymes [BR:sas01000] 1. Oxidoreductases  1.1  Acting on…

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Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus

Bacteriophage isolation Streptomyces phages Vanseggelen and Verabelle were isolated from a soil sample obtained from the National Park Zuid-Kennemerland in the Netherlands (N52° 23′ 31″, E4° 34′ 49″) using Streptomyces coelicolor as the host. Details on isolation procedures are reported previously in detail12. The collected phage stock solutions were stored…

Continue Reading Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus

KEGG T00918: Mlut_12280

Entry Mlut_12280        CDS       T00918                                  Name (GenBank) Undecaprenyl pyrophosphate synthetase   KO K00806   undecaprenyl diphosphate synthase [EC:2.5.1.31] Organism mlu  Micrococcus luteus Pathway mlu00550   Peptidoglycan biosynthesis mlu00900   Terpenoid backbone biosynthesis mlu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:mlu00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00550 Peptidoglycan biosynthesis    Mlut_12280  09109 Metabolism of terpenoids and polyketides   00900 Terpenoid backbone biosynthesis    Mlut_12280 09180 Brite…

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KEGG T00139: BP3287

Entry BP3287            CDS       T00139                                  Symbol atpG Name (GenBank) ATP synthase gamma chain   KO K02115   F-type H+-transporting ATPase subunit gamma Organism bpe  Bordetella pertussis Tohama I Pathway bpe00190   Oxidative phosphorylation bpe01100   Metabolic pathways Module bpe_M00157   F-type ATPase, prokaryotes and chloroplasts Brite KEGG Orthology (KO) [BR:bpe00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BP3287 (atpG) 09180 Brite Hierarchies  09181 Protein…

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CHEM271 Genbank – CHEM 271 WINTER 2016 GENBANK ASSIGNMENT Name: ID#: Please answer the questions on

CHEM 271 WINTER 2016 GENBANK ASSIGNMENT Name: ID#: Please answer the questions on this page ONLY, including the back, when necessary 1. Alpha-1 antitrypsin from what organism is defined by accession number NP_001121179.1? Organism: Homo Sapiens 2. How many amino acids does accession number NP_001121179.1 have? The accession number contains…

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Ref seq/Gene bank accession to Entrez id for cluster profiler

Ref seq/Gene bank accession to Entrez id for cluster profiler 1 I have a list id of GenBank accession (protein) for different bacterial species (these are non model bacterial species). The next step is to do GSEA for these proteins. I tried to convert GenBank accession to entrez id, But…

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GenBank

GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data…

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Detection of Clostridium perfringens Using Novel Methods Based on Recombinase-Aided Amplification Assay-Assisted CRISPR/Cas12a System

Clostridium perfringens is a highly versatile pathogen of humans and animals. Rapid and sensitive detection methods for C. perfringens are urgently needed for the timely implementation of control. In this study, to provide novel promising methods for the detection of C. perfringens, two rapid, sensitive, and instrument-free C. perfringens detection…

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The expanding range of emerging tick-borne viruses in Eastern Europe and the Black Sea Region

Our pooled and individual metagenome-based tick screening using NS revealed 25 virus taxa including four tick-borne pathogens in samples collected from countries from Eastern Europe and around the Black Sea. Known tick-borne viruses endemic in the region, such as CCHFV or TBEV, were not detected, owing to the low prevalence…

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Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

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TP06 How to download sequences from Genbank – Downloading sequences from Genbank Genbank is a major

Downloading sequences from Genbank Genbank is a major resource for biological sequence data. Genbank is available online through a web interface. This guide describes how to download a sequence file or a part of a sequence file from genbank given an accession number or an accession number and start and…

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Solved In this problem, we will use Biopython to translate

In this problem, we will use Biopython to translate the CDS (CoDing Squence) sequence(s) in GenBank file. First, use the retrieve_GenBank_info(id) (from the lecture notw, also given below) to save the GenBank record of Helicobacter pylori 26695. id is the id of helicobactor you found in Problem 3. Make sure…

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Bioconductor – GeneR

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see GeneR. R for genes and sequences analysis Bioconductor version: 2.8 Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) Author: L. Cottret, A. Lucas <antoinelucas at gmail.com>, E. Marrakchi, O. Rogier, V. Lefort, P. Durosay,…

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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KEGG T00186: ECA0055

Entry ECA0055           CDS       T00186                                  Symbol prlC Name (GenBank) oligopeptidase A   KO K01414   oligopeptidase A [EC:3.4.24.70] Organism eca  Pectobacterium atrosepticum SCRI1043 Brite KEGG Orthology (KO) [BR:eca00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:eca01002]    ECA0055 (prlC)Enzymes [BR:eca01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.24  Metalloendopeptidases    3.4.24.70  oligopeptidase A     ECA0055 (prlC)Peptidases and inhibitors [BR:eca01002] Metallo peptidases  Family M3   ECA0055 (prlC) BRITE hierarchy SSDB OrthologParalogGene…

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KEGG T00644: APJL_0327

Entry APJL_0327         CDS       T00644                                  Symbol rumA Name (GenBank) 23S rRNA (Uracil-5-)-methyltransferase   KO K03215   23S rRNA (uracil1939-C5)-methyltransferase [EC:2.1.1.190] Organism apj  Actinobacillus pleuropneumoniae JL03 (serotype 3) Brite KEGG Orthology (KO) [BR:apj00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03009 Ribosome biogenesis [BR:apj03009]    APJL_0327 (rumA)Enzymes [BR:apj01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.190  23S rRNA (uracil1939-C5)-methyltransferase     APJL_0327 (rumA)Ribosome biogenesis [BR:apj03009] Prokaryotic type  rRNA modification factors   23S rRNA…

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Solved Problem 2 In the class, we wrote a function

Problem 2 In the class, we wrote a function retrieve_GenBank_info(id) that retrieves a sequence information in the GenBank format from NCBI, saves it into a file, and returns the requence. In this problem, your task is to convert this function to retrieve_FASTA_info(id) that retreives a sequence in the fasta format,…

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Bioconductor – rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

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KEGG T00186: ECA2422

Entry ECA2422           CDS       T00186                                  Symbol thrS Name (GenBank) threonyl-tRNA synthetase   KO K01868   threonyl-tRNA synthetase [EC:6.1.1.3] Organism eca  Pectobacterium atrosepticum SCRI1043 Pathway eca00970   Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:eca00001] 09120 Genetic Information Processing  09122 Translation   00970 Aminoacyl-tRNA biosynthesis    ECA2422 (thrS) 09180 Brite Hierarchies  09181 Protein families: metabolism   01007 Amino acid related enzymes [BR:eca01007]    ECA2422 (thrS)  09182 Protein families: genetic information processing   03016 Transfer…

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