Tag: GenBank

getphylo: rapid and automatic generation of multi-locus phylogentic trees from genbank files

Abstract Phylogenetic trees are the primary tool for visualising evolutionary relationships. Traditionally, phylogenies are inferred from manually curated sets of marker genes. As available genomic data increases, there is increasing demand for tools to automatically build phylogeny from assembled genomes. Existing tools rely on reference databases of preselected marker genes,…

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Rapid gene content turnover on the germline-restricted chromosome in songbirds

This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…

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Illumina short-read genome sequencing of knockout mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

Description: This dataset contains sequencing reads of the wild type strain S. suis P1/7 and two knockout mutants constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and one 5bp deletion relative to the reference…

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Characterization of the two tandem repeats for the KPC-2 core structures on a plasmid from hospital-derived Klebsiella pneumoniae

Antimicrobial susceptibility test, enzymatic property, and transferrable feature The 16S rRNA sequence and species identification of strain F94 as Klebsiella pneumoniae were confirmed using BLAST and average nucleotide homology analysis of the genomic sequence. Results for the drug-susceptibility test of F94 strain were shown in Table 1. In particular, the…

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SeqCode Provides Path to Name Uncultivated Prokaryotes

The name elephant. Investigators from different disciplines examine different portions of a microorganism and develop their own opinions about its nature. Precise scientific names enable the unification of information from disparate disciplines and laboratories to create a single, multifaceted vision. Source: William Whitman and Brian Hedlund Most prokaryotes have never…

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Age-related self-DNA accumulation may accelerate arthritis in rats and in human rheumatoid arthritis

Statement of ethics and regulations Our clinical data collection was approved by the Research Ethics Committee of the Affiliated Hospital of Southwest Medical University (KY 2021010). The animal study was conducted according to the guidelines of the Institutional Animal Care and Use Committee of Macau University of Science and Technology…

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Insertion sequence transposition inactivates CRISPR-Cas immunity

Primers, plasmids, bacterial strains, and growth conditions Primers, plasmids, and strains used in this study are listed in Tables S1–S3, respectively. Escherichia coli strains MG1655, DH10B, MDS42, and their derivates were cultured in LB medium at 37 °C, with shaking at 220 rpm. All the recombinants containing the temperature-sensitive pSC101-derived plasmid were cultured…

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Cervical carcinogenesis risk association of HPV33 E6 and E7 genetic variations in Taizhou, Southeast China | Virology Journal

Characteristics of the study population From February 2014 to December 2020, a total of 189 women with a single HPV33 infection were selected. The average age was 42.3 years (range 19–73 years). A total of 185 (97.9%) sequences of the entire E6 and E7 genes from HPV33 were successfully obtained….

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Help with htseq -count read counts

Hello I am doing a transcriptome analysis on Pseudomonas putida and I have been trying to do a read count using Htseq -count. The program always give an error. I have tried different genome references (fna) and annotation files (gtf ang gff) but it does not work. The mapping works…

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Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Isolation of crAss-like phages CrAss-like phages were searched in 12 sewage samples from five wastewater treatment plants using three different qPCR assays, the one designed from ΦCrAss001 genome in this study and two previously described12,19. Depending on the qPCR assay employed and the samples, values in wastewater ranged from 103−106…

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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…

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Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

Animals and cells Adult amphioxus B. japonicum collected from the sandy bottom of the sea near Qingdao, China, were cultured in aerated seawater at room temperature and fed with single-celled algae once a day. Zebrafish (D. rerio) aged 3 months and adult Japanese scallops (M. yessoensis) were purchased from Nanshan…

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Conservation of Nirsevimab Binding Sites in RSV Fusion Glycoprotein

The following is a summary of “Nirsevimab binding-site conservation in respiratory syncytial virus fusion glycoprotein worldwide between 1956 and 2021: an analysis of observational study sequencing data,” published in the June 2023 issue of the Infectious Diseases by Wilkins et al. Nirsevimab is a monoclonal antibody with an extended half-life…

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Introduction to Biopython

The powerful bioinformatics programme Biopython has become a standard resource for experts in the area. You are given an introduction to Biopython in this article, which also covers its installation and provides examples that demonstrate its use. Even though we’re going into Biopython, remember that it’s only a small part…

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HMM gets zero or 1 hits when many more expected

HMM gets zero or 1 hits when many more expected 1 Hi all, My ultimate goal is to understand the phylogeny of a set of restriction-modification enzymes among certain genomes. For this, I have done the following: Downloaded all RM genes DNA sequences into psych_rm_genes.fna from REBASE Cleaned rebase file…

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ASM338422v1 – Assembly – CNGBdb

 Home Assembly GCF_003384225.1 Assembly ID: – Source: RefSeq Assembly ( ID GCF_003384225.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

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is a bioinformatics certificate worth it

Application criteria may vary depending on the program you wish to be admitted to. Microbiology Course. Hello all, I have a BS in molecular biology, and after working for a bit and dipping my feet in the wet lab, I realize it is not the place I want to be….

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A geopositioned and evidence-graded pan-species compendium of Mayaro virus occurrence

Anderson, C. R., Downs, W. G., Wattley, G. H., Ahin, N. W. & Reese, A. A. Mayaro virus: a new human disease agent. II. Isolation from blood of patients in Trinidad, B.W.I. Am. J. Trop. Med. Hyg. 6, 1012–1016, doi.org/10.4269/ajtmh.1957.6.1012 (1957). Article  CAS  PubMed  Google Scholar  Causey, O. R. &…

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Successful treatment with doxycycline monotherapy for human infection with Babesia venatorum (Babesiidae, Sporozoa) in China: a case report and proposal for a clinical regimen | Infectious Diseases of Poverty

Clinical course of the case A 73-year-old male underwent splenectomy after a traffic accident in 2014, and blood transfusion was performed during surgery. He had no history suggestive of any chronic diseases, or drug or alcohol abuse. The patient, with no recorded family history, had quit smoking 10 years ago…

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Isolation and genome characterization of Lloviu virus from Italian Schreibers’s bats

Ethics and biosafety statement Bats were captured during the day with hand-nets in full compliance with best practice and national and European regulations, in derogation to the Council Directive 92/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora (authorization 38,025 of 13/08/2020…

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NOAA, FDA release DNA barcode library to identify fish

A team of researchers from NOAA, the Food and Drug Administration, and other partners have released the first batch of fish DNA barcodes, curated DNA sequences that can be used to identify and authenticate seafood. NOAA, the FDA, the Smithsonian Institution, and the Philippine National Fisheries Research and Development Institute…

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Sci-Hub | Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification. Scientific Reports, 11(1)

Sci-Hub | Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification. Scientific Reports, 11(1) | 10.1038/s41598-021-82385-z ◂ ↓ save Wu, H.-Y., Chan, K.-T., But, G. W.-C., & Shaw, P.-C. (2021). Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification. Scientific Reports, 11(1)….

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Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group

Isolate storage, growth, and identification Historical BFG isolates originally cultured from clinical material between 1973 and 2018 were stored either lyophilized or frozen in skim milk media at the National Institutes of Health Clinical Center Department of Laboratory Medicine (Bethesda, MD). Isolates were de-identified and metadata including year and source/site…

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KEGG T01776: PMCN06_1106

Entry PMCN06_1106       CDS       T01776                                  Symbol mtnN Name (GenBank) 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase   KO K01243   adenosylhomocysteine nucleosidase [EC:3.2.2.9] Organism pmv  Pasteurella multocida subsp. multocida HN06 Pathway pmv00270   Cysteine and methionine metabolism pmv01100   Metabolic pathways pmv01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:pmv00001] 09100 Metabolism  09105 Amino acid metabolism   00270 Cysteine and methionine metabolism    PMCN06_1106 (mtnN)Enzymes [BR:pmv01000] 3. Hydrolases  3.2  Glycosylases   3.2.2  Hydrolysing N-glycosyl…

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BLAST Tools: asn2gb????

BLAST Tools: asn2gb???? 1 Hi guys Does anyone have any experience in running BLAST Tools asn2gb which converts .asn files to genbank? I am struggling to get mine running and would love to see an example of a script or any such thing please?! Thanks! asn2gb BLAST-Tools • 1.4k views…

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KEGG T03465: KPNIH29_22470

Entry KPNIH29_22470     CDS       T03465                                  Name (GenBank) adenine glycosylase   KO K03575   A/G-specific adenine glycosylase [EC:3.2.2.31] Organism kpv  Klebsiella pneumoniae subsp. pneumoniae KPNIH29 Pathway kpv03410   Base excision repair Brite KEGG Orthology (KO) [BR:kpv00001] 09120 Genetic Information Processing  09124 Replication and repair   03410 Base excision repair    KPNIH29_22470 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03400 DNA repair and recombination proteins [BR:kpv03400]    KPNIH29_22470Enzymes…

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Identification of bacterial isolates of Tumpang and Bumiasri (East Java, Indonesia) using 16S rRNA gene sequencing and screening of their active compounds as a biofertilizer

Prihartini, Indah and Ismail, Akhis Soleh and Sukorini, Henik and Nursandi, Fatimah and Zakia, Aulia and Farahdina, Farusa Anggita Risyawal (2023) Identification of bacterial isolates of Tumpang and Bumiasri (East Java, Indonesia) using 16S rRNA gene sequencing and screening of their active compounds as a biofertilizer. BIODIVERSITAS, 24 (6). pp….

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bioinformatics coach github

During practicals, when you are done, please press the green Yes button: This way we will know when we can move on. Organizer – Bioinformatics Core at UC Davis This tool searches for code cited in PubMed abstracts by searching for popular repositories such as GitHub and Bitbucket. This repository…

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ASM360979v1 – Assembly – CNGBdb

 Home Assembly GCA_003609795.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_003609795.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

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C. ramosum in immunocompetent patient with SARS-CoV-2

Introduction Clostridium ramosum was first identified and characterized in 1898 following its isolation from a patient with pulmonary gangrene and appendicitis.1 This species, initially identified as Bacillus ramosum and later referred to as C. ramosum, was renamed Erysipelatoclostridium ramosum in 2013.2 However, its taxonomic name has not been legally published…

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Morphology and genetic characterization of Physaloptera sibirica Petrow & Gorbunov, 1931 (Spirurida: Physalopteridae), from the hog-badger Arctonyx collaris Cuvier (Carnivora: Mustelidae), with molecular phylogeny of Physalopteridae | Parasites & Vectors

Order Spirurida Railliet, 1914 Superfamily Physalopteroidea Railliet, 1893 Family Physalopteridae Railliet, 1893 Genus Physaloptera Rudolphi, 1819 Physaloptera sibirica Petrow & Gorbunow, 1931 Host: The hog badger Arctonyx collaris Cuvier (Carnivora: Mustelidae). Locality: Shaanxi Province, China. Site of infection: Stomach. Specimen deposition: 5 males, 10 females (HBNU-N-2022M1120-CL); deposited at the College…

Continue Reading Morphology and genetic characterization of Physaloptera sibirica Petrow & Gorbunov, 1931 (Spirurida: Physalopteridae), from the hog-badger Arctonyx collaris Cuvier (Carnivora: Mustelidae), with molecular phylogeny of Physalopteridae | Parasites & Vectors

Senior Bioinformatics Scientist – Cepheid

Senior Bioinformatics Engineer – Biochip R&D Group Cepheid Location Sunnyvale, California, United States of America At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex…

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Characterization of 28S rRNA sequences of cestoda parasite Electrotaenia malapteruri Fritsch, 1886 from the Electric catfish Malapterurus electricus (Siluriformes: Malapteruridae)

Proteocephalids are cestoda parasites that mostly infect freshwater fish. The present study was carried out to investigate the presence of proteocephalids infecting the electric catfish Malapterurus electricus from Lake Manzala, Kafr El-Sheikh Governorate, Egypt. Morphological characterization revealed the present parasite is a cestoda belonging to the genus Electrotaenia. Morphologically, the…

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CD70 shRNA Plasmid Human) – Gentaur.com

Catalog number MBS8250746 Price Please ask Size 0,15 mg Other size please contact us to order other different size Properties Human proteins, cDNA and human recombinants are used in human reactive ELISA kits and to produce anti-human mono and polyclonal antibodies. Modern humans (Homo sapiens, primarily ssp. Homo sapiens sapiens). Depending on the epitopes…

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KEGG T06565: PC2016_3200

Entry PC2016_3200       CDS       T06565                                  Name (GenBank) DNA polymerase V   KO K03503   DNA polymerase V [EC:3.4.21.-] Organism pcar  Pseudoalteromonas carrageenovora Brite KEGG Orthology (KO) [BR:pcar00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:pcar01002]    PC2016_3200  09182 Protein families: genetic information processing   03400 DNA repair and recombination proteins [BR:pcar03400]    PC2016_3200Enzymes [BR:pcar01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.21  Serine endopeptidases    3.4.21.-     PC2016_3200Peptidases and inhibitors…

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EMDB < EMD-33674

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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How to solve this error in the “read.gb” R function?

How to solve this error in the “read.gb” R function? 1 So I am trying to read a file with the extension “gb”, that a downloaded directly from the website. I am using the “read.gb” function: library(read.gb) df<-read.gb(“sequence.gb”,Type = “full”, Source = “File”) I thought it would be straightfoward, and…

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Mitochondrial DNA is a target of HBV integration

Patients Tumour tissues from seven HBsAg-positive patients (6 men, 1 woman; mean age 66.7 ± 8 years) with HBV-related HCC and paired adjacent non-tumour tissues from six of them were studied. The clinical, histological, and virologic characteristics of the patients are summarised in Table 1. Two normal liver samples from HBV-negative patients who…

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Deoxyribonucleic Acid Barcoding for the Identification of Botanicals

Hebert PD, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312 CrossRef  PubMed  PubMed Central  Google Scholar  International Barcode of Life Conference (2011) www.dnabarcodes2011.org/ China Plant BOL Group, Li DZ, Gao LM, Li HT, Wang H, Ge XJ, Liu JQ, Chen ZD, Zhou…

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Exploration of multi-gene DNA barcode markers to reveal the broad genetic diversity of field ticks (Acari: Ixodidae) in a tropical environment of Hainan Island, China

Ticks are haematophagous arthropods and obligate ectoparasites of humans and other animals. This study focused on the molecular discrimination of ticks in the tropical environment of Hainan according to multi-gene DNA barcode markers with the expectation of accurately distinguishing species. A total of 420 ticks, including 49 adult ticks, 203…

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S2043 – Assembly – CNGBdb

 Home Assembly GCA_000967485.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_000967485.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

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ASM433591v1 – Assembly – CNGBdb

 Home Assembly GCA_004335915.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_004335915.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

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Georgetown Researchers Call for Improved Pathogen Genomic Data Sharing

NEW YORK — Researchers at Georgetown University have outlined strategies for improving the sharing of pathogen genomic sequencing data in order to ensure better preparedness for future pandemics. In a commentary published in the New England Journal of Medicine on Wednesday, they noted that in past outbreaks, sharing of pathogen genome sequences was often delayed….

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Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

Sumario: Abstract We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens’ identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit…

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GenBank Release 256.0 is Available!

Genbank release 256.0 (6/21/2023) is now available on the NCBI FTP site. This release has 24.45 trillion bases and 3.66 billion records. During the 63 days between the close dates for GenBank Releases 255.0 and 256.0, the traditional portion of GenBank grew by 139,733,657,333 base pairs and by 1,005,927 sequence…

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Agronomy | Free Full-Text | Construction and Functional Evaluation of CRISPR/Cas9 Multiple Knockout Vectors of the FAD2 Gene Family

1. Introduction Soybean (Glycine max (Linn.) Merr.) originated from China and is one of the most important legume and oil crops in the world [1]. The index evaluation of soybean oil is mainly related to the content and composition ratios of five fatty acids: oleic acid (C18:1), linoleic acid (C18:2),…

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LOC127890413 H3K27ac hESC enhancers GRCh37_chr19:10362245-10362818 and GRCh37_chr19:10362819-10363392 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

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Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

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KEGG T04356: MYVA_2452

Entry MYVA_2452         CDS       T04356                                  Name (GenBank) diadenosine polyphosphate hydrolase   KO K19710   ATP adenylyltransferase [EC:2.7.7.53] Organism mvq  Mycolicibacterium vaccae Pathway mvq00230   Purine metabolism mvq01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:mvq00001] 09100 Metabolism  09104 Nucleotide metabolism   00230 Purine metabolism    MYVA_2452Enzymes [BR:mvq01000] 2. Transferases  2.7  Transferring phosphorus-containing groups   2.7.7  Nucleotidyltransferases    2.7.7.53  ATP adenylyltransferase     MYVA_2452 BRITE hierarchyBRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  HIT DcpS_C CwfJ_C_1 Motif Other…

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Impact of nanopore-based metagenome sequencing on tick-borne virus detection

. 2023 May 30;14:1177651. doi: 10.3389/fmicb.2023.1177651. eCollection 2023. Koray Ergunay  1   2   3   4 , Ender Dincer  5 , Silvia A Justi  1   2   3 , Brian P Bourke  1   2   3 , Suppaluck P Nelson  1   2   3 , Hsiao-Mei Liao  6   7 , Mehmet…

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KEGG T06049: FHG12_17955

Entry FHG12_17955       CDS       T06049                                  Name (GenBank) lactonase family protein   KO K07404   6-phosphogluconolactonase [EC:3.1.1.31] Organism hyj  Hymenobacter jejuensis Pathway hyj00030   Pentose phosphate pathway hyj01100   Metabolic pathways hyj01110   Biosynthesis of secondary metabolites hyj01120   Microbial metabolism in diverse environments hyj01200   Carbon metabolism Module hyj_M00004   Pentose phosphate pathway (Pentose phosphate cycle) hyj_M00006   Pentose phosphate pathway, oxidative phase,…

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Pseudogene identification from Fish genome

Forum:Pseudogene identification from Fish genome 0 Hi, I have been working on finding pseudogenes from clarias magur genome assembly available in genbank which is assembled to scaffold level and not to chromosome level. There is also protein fasta file of the assembly in the Genbank. I want to find pseudogenes…

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How Gene Sequencing Will Power Truly Personalized Medicine

Gene sequencing technology has come a long way since its inception. In the early days, it took years and millions of dollars to sequence just a single genome. But today, thanks to advances in technology and an open source mindset, gene sequencing has become more accurate and accessible than ever…

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How to retrieve gene and CDS entries properly from GenBank files with Perl?

In my goal to write a Perl script without modules that retrieves all simple gene and CDS entries (without the GenBank operators, since I have no clue how to handle them) in a specified range, I’ve come up with the following: use strict; use warnings; my $gene=””; my $CDS =…

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Genbank assignment W2023 Final – CHEM 271 – Concordia

CHEM 271 WINTER 2023 GENBANK ASSIGNMENT Name:_________________________ ID#:___________________________ Please answer the questions on this page ONLY, including the back, when necessary 1. Phospholipase A2 from what organism is defined by accession number AAF09020.1? (0.5 mark) 2. How many amino acids does the protein assigned accession number AAF09020.1 have? (0.5 mark)…

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A novel Rickettsia, Candidatus Rickettsia takensis, and the first record of Candidatus Rickettsia laoensis in Dermacentor from Northwestern Thailand

More than 40 species of Dermacentor ticks are known worldwide23,24,25. So far, eight species (D. auratus, D. compactus, D. steini, D. filippovae, D. pasteuri, D. laothaiensis, D. falsosteini, and D. tricuspis) have been found in Thailand24,25,26,27,28. Of these, three species were morphologically and molecularly identified as D. laothaiensis, D. steini,…

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Automatically construct a genus-level data matrix using sequences from GEBANK, for phylogenetic analyses

Automatically construct a genus-level data matrix using sequences from GEBANK, for phylogenetic analyses 0 Hi everyone, I want to use the sequences from NCBI GENBANK to build a genus-level datamatrix for an order, which has about 40 families and 30000 genera. There are many methods/software that can download sequences from…

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2023 Warren Alpert Prize Honors Pioneer in Computational Biology

“At a time when computation was deemed an exotic pursuit by most biomedical researchers, David was prescient because he understood the potential of computation to propel biomedical science forward,” said George Q. Daley, dean of HMS and chair of the Warren Alpert Foundation Prize scientific advisory board. “His vision, creativity,…

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Ombudsman urged to resolve graft raps vs former BSP-MB execs

THE son of the former owners of General Bank and Trust Company (GBTC or GenBank) has asked the Office of the Ombudsman to resolve the 10-year-old criminal complaint filed by their family against former Bangko Sentral ng Pilipinas (BSP) governor and Monetary Board chairman Amando Tetangco Jr. and eight other…

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Selecting CDS from genbank file interval

Selecting CDS from genbank file interval 0 Hello, I tried writing a script in perl that extracts from two parameters the CDS portions with their description and output them in a .txt file, but it just comes out empty. Help! #!/usr/bin/perl use strict; use warnings; # Get the interval data…

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seq2R source: R/read.genbank.R

read.genbank <- function (locus) { X <- character() URL <- paste(“http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=”,paste(locus, collapse = “,”), “&rettype=gb&retmode=text”,sep = “”) X <- c(X, scan(file = URL, what = “”, sep = “\n”, quiet = TRUE)) prin <- grep(“^ {0,}ORIGIN”, X) + 1 fin<- which(X == “//”) – 1 res <- list() code <-…

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KEGG T02974: Y013_10995

Entry Y013_10995        CDS       T02974                                  Name (GenBank) ATPase   KO K01533   P-type Cu2+ transporter [EC:7.2.2.9] Organism rpy  Rhodococcus pyridinivorans SB3094 Brite KEGG Orthology (KO) [BR:rpy00001] 09190 Not Included in Pathway or Brite  09191 Unclassified: metabolism   99980 Enzymes with EC numbers    Y013_10995Enzymes [BR:rpy01000] 7. Translocases  7.2  Catalysing the translocation of inorganic cations   7.2.2  Linked to the hydrolysis of a nucleoside triphosphate    7.2.2.9  P-type Cu2+ transporter     Y013_10995 BRITE hierarchyBRITE…

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KEGG T02874: DT104_21531

Entry DT104_21531       CDS       T02874                                  Symbol rfbC Name (GenBank) dTDP-4-dehydrorhamnose 3,5-epimerase   KO K01790   dTDP-4-dehydrorhamnose 3,5-epimerase [EC:5.1.3.13] Organism send  Salmonella enterica subsp. enterica serovar Typhimurium DT104 Pathway send00521   Streptomycin biosynthesis send00523   Polyketide sugar unit biosynthesis send00541   O-Antigen nucleotide sugar biosynthesis send01100   Metabolic pathways send01110   Biosynthesis of secondary metabolites send01250   Biosynthesis of nucleotide sugars Module send_M00793  …

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Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

Fungal genomic DNA DNA extracted from Aspergillus niger (kindly provided by Dr. Takamitsu Imoto, Medical Research Institute, Kitano Hospital, Osaka, Japan) and a mock community DNA standard (Mycobiome Genomic DNA Mix, MSA-1010; ATCC, Manassas, VA, USA) were used to evaluate the validity of the sequencing methodology. The mock community standard…

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Visualize mitochondrial genome

Visualize mitochondrial genome 1 Hi all, I have a simple question. I want to visualize the mitochondrial genome together with its genes, the typical image that you find when you look for mitochondrial genome at google: www.ecosia.org/images?q=mitochonrial%20genome I already have the fasta file and the annotation done and I have…

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Antibiotics | Free Full-Text | Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates

1. Introduction Filifactor alocis is an obligate anaerobic, non-sporeforming, Gram-positive rod [1,2]. This microorganism was first described in 1985 after being isolated from patients with periodontitis or gingivitis [3]. However, it was not until the early to mid-2000s, with the improvement of molecular identification techniques, when F. alocis was first…

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Bacterial DNA metabolism analysis by metagenomic next-generation sequencing (mNGS) after treatment of bloodstream infection | BMC Infectious Diseases

Animals Adult New Zealand rabbits (male, 2.0-2.5 kg) were purchased from Guangdong Medical Laboratory Animal Center. The rabbits were reared in experimental conditions (temperature, 20–25 °C; humidity, 50–70%) with a 12 h light/dark cycle and fed standard chow and water. All of the rabbits were injected with the inactivated E. coli. Bacteria The…

Continue Reading Bacterial DNA metabolism analysis by metagenomic next-generation sequencing (mNGS) after treatment of bloodstream infection | BMC Infectious Diseases

Characteristics of molecular markers associated with chloroquine resistance in Plasmodium vivax strains from vivax malaria cases in Yunnan Province, China | Malaria Journal

Sample amplification information and PCR product amplification sequencing A total of 753 cases infected with mono-P. vivax were diagnosed and confirmed in Yunnan Province in 2014, 2020, 2021, and 2022. The patients were predominantly young adult males (84.0%, 632/753), with a smaller number of females (16.0%, 121/753); 81.8% (616/753) of…

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Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera)

“I have just been thinking, and I have come to a very important decision. These are the wrong sort of bees.”—Winnie the Pooh. A mitogenomic phylogeography of species of Apis and subspecies of Apis mellifera The mitogenomic analysis confirms with high confidence previous inferences as to morpho-behavioral relationships among nine…

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read.GenBank function – RDocumentation

The function uses the site www.ncbi.nlm.nih.gov/ from where the sequences are retrieved. If species.names = TRUE, the returned list has an attribute “species” containing the names of the species taken from the field “ORGANISM” in GenBank. Since ape 3.6, this function retrieves the sequences in FASTA format: this is more…

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Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness

Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…

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KEGG T00166: LIC_12265

Entry LIC_12265         CDS       T00166                                  Name (GenBank) conserved hypothetical protein   KO K21472   peptidoglycan LD-endopeptidase LytH [EC:3.4.-.-] Organism lic  Leptospira interrogans serovar Copenhageni Brite KEGG Orthology (KO) [BR:lic00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:lic01002]    LIC_12265   01011 Peptidoglycan biosynthesis and degradation proteins [BR:lic01011]    LIC_12265Enzymes [BR:lic01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.-    3.4.-.-     LIC_12265Peptidases and inhibitors [BR:lic01002] Metallo peptidases  Family M23   LIC_12265Peptidoglycan biosynthesis…

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Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR

Wanyang Dong,1,&ast; Qi Peng,1,&ast; Xiaohua Tang,1,2,&ast; 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…

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Class B1 GPCR activation by an intracellular agonist

Expression and purification of human PTH1R The plasmid encoding human PTH1R (GenBank identifier: U17418.1; residues 27–491) was constructed and purified as previously reported17. The construct was expressed in HEK293 GnTI (N-acetylglucosaminyltransferase I-negative) cells (American Type Culture Collection, CRL-3022) using the BacMam system (Thermo Fisher Scientific), and the cells were grown…

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Genomic characteristics of ESBL-producing E. coli in China

Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…

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KEGG T00661: FMG_0425

Entry FMG_0425          CDS       T00661                                  Name (GenBank) glycine reductase complex selenoprotein   KO K21577   glycine/sarcosine/betaine reductase complex component C subunit beta [EC:1.21.4.2 1.21.4.3 1.21.4.4] Organism fma  Finegoldia magna Brite KEGG Orthology (KO) [BR:fma00001] 09190 Not Included in Pathway or Brite  09191 Unclassified: metabolism   99980 Enzymes with EC numbers    FMG_0425Enzymes [BR:fma01000] 1. Oxidoreductases  1.21  Catalysing the reaction X-H + Y-H = X-Y   1.21.4  With a…

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KEGG T07081: G7082_08800

Entry G7082_08800       CDS       T07081                                  Name (GenBank) glycine reductase   KO K21577   glycine/sarcosine/betaine reductase complex component C subunit beta [EC:1.21.4.2 1.21.4.3 1.21.4.4] Organism vhy  Vagococcus hydrophili Brite KEGG Orthology (KO) [BR:vhy00001] 09190 Not Included in Pathway or Brite  09191 Unclassified: metabolism   99980 Enzymes with EC numbers    G7082_08800Enzymes [BR:vhy01000] 1. Oxidoreductases  1.21  Catalysing the reaction X-H + Y-H = X-Y   1.21.4  With a disulfide as…

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Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach

The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of…

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LOINC 87396-8 GenBank accession number

Term Description The unique identifier assigned to an organism-specific genetic sequence submitted to a reference database such as GenBank (www.ncbi.nlm.nih.gov/genbank/). GenBank identifiers are called Accession numbers, and GenBank includes sequence data for a variety of organisms, including humans, other animals, plants, and microorganisms. Source: Regenstrief LOINC Fully-Specified Name Component GenBank…

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Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…

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Gap-free genome assembly of anadromous Coilia nasus

Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS  Google Scholar  Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…

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A Guide to DNA Sequencers

DNA sequencing is a method that determines the order of the four nucleotide bases, namely, adenine (A), thymine (T), guanine (G), and cytosine (C), that form a DNA molecule. In this article, AZoLifeSciences offers a comprehensive guide to DNA Sequencers. Image Credit: Blue Andy/Shutterstock.com In a DNA double helix, nucleotide bases…

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A Short History of Virology

This article is pulled from the 15 day Troubles Away program of short videos and games designed to remove troubles from your life.  Considering recent global events does a short history of virology support the central insight of Troubles Away, namely that troubles appear when we believe in something that…

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Characterization of nuclear DNA diversity in an individual Leymus chinensis

Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…

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Solved You decide the best place to start would be the

You decide the best place to start would be the “Gene” database of the National Center for Biotechnology Information, also known as “GenBank”. You go to GenBank, select “Gene” from the database dropdown menu and input “SBE1” into the search function. a) How many results come up? The top two…

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Accidental DNA collection by air sensors could revolutionize wildlife tracking

An air-quality monitoring station in London is located near a deer park, so it picks up DNA from species such as Dama dama (fallow deer) in its filters.Credit: Robert Knell Scientists might be able to keep tabs on the world’s flora and fauna by analysing DNA floating through the air….

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Perl. How to retrieve data until a keyword in GenBank?

Perl. How to retrieve data until a keyword in GenBank? 0 Hello! I’m trying to write a script that retrieves data from GenBank files. I need only the info until the COMMENT part of the annotation. This is my INPUT: LOCUS mitochondrion_genome 19524 bp DNA HTG 17-DEC-2022 DEFINITION Drosophila melanogaster…

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Genomic characteristics of a multidrug-resistant E. coli

Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…

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Characterization of metagenome-assembled genomes from the International Space Station | Microbiome

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

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LOC127888533 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

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Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

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KEGG T01170: Kvar_3615

Entry Kvar_3615         CDS       T01170                                  Name (GenBank) galactose-1-phosphate uridylyltransferase   KO K00965   UDPglucose–hexose-1-phosphate uridylyltransferase [EC:2.7.7.12] Organism kva  Klebsiella variicola At-22 Pathway kva00052   Galactose metabolism kva00520   Amino sugar and nucleotide sugar metabolism kva01100   Metabolic pathways kva01250   Biosynthesis of nucleotide sugars Module kva_M00554   Nucleotide sugar biosynthesis, galactose => UDP-galactose kva_M00632   Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P…

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Why aren’t authors specific about patch version?

I am finding difficulty finding the exact assembly version (e.g. patch version) of GRCh38 used for major databases. For instance, gnomad says “GRCh38”. But the only information on the version, for v3.1 comes from here, which says it “uses an updated version of Variant Effect Predictor (VEP) based on the…

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Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

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Answered: What is GenBank ?

1 A Perspective On Human Genetics2 Cells And Cell Division3 Transmission Of Genes From Generation To Generation4 Pedigree Analysis In Human Genetics5 The Inheritance Of Complex Traits6 Cytogenetics: Karyotypes And Chromosome Aberrations7 Development And Sex Determination8 The Structure, Replication, And Chromosomal Organization Of Dna9 Gene Expression And Gene Regulation10 From…

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What Are The Most Common Stupid Mistakes In Bioinformatics?

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

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KEGG T04088: AOZ06_32105

Entry AOZ06_32105       CDS       T04088                                  Name (GenBank) hypothetical protein   KO K05553   minimal PKS acyl carrier protein Organism kphy  Kibdelosporangium phytohabitans Pathway kphy01056   Biosynthesis of type II polyketide backbone kphy01100   Metabolic pathways kphy01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:kphy00001] 09100 Metabolism  09109 Metabolism of terpenoids and polyketides   01056 Biosynthesis of type II polyketide backbone    AOZ06_32105   00253 Tetracycline…

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EMDB < EMD-17118

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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biopython – Why does my for loop in Python never stop running?

I am creating a code that takes accession numbers from an existing excel file and ultimately running it through BLAST using Entrez. I am very new to Python and pretty much just learning as a I write. Here is what my code looks like right now, it currently will run…

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ZNF330/NOA36 interacts with HSPA1 and HSPA8 and modulates cell cycle and proliferation in response to heat shock in HEK293 cells | Biology Direct

Cell lines, culture conditions, heat shock treatment and transfections HeLa, HEK293 and 2D12 (a NOA36-knockout HEK293-cell line generated in this work) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a CO2 incubator. For heat…

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