Categories
Tag: GCA
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…
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,…
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…
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…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
Phenotypic profiling of solute carriers characterizes serine transport in cancer
Cell culture All cell lines used in this study were cultured at 37 °C in 5% CO2 in a humidified incubator. Human cell lines were authenticated by STR profiling using Promega GenePrint 10 and tested for Mycoplasma using Mycoalert (Lonza). Other than HCT116 p21−/− (a gift of B. Vogelstein60) all cell…
How to download multiple genome files using command line (MacOS) using datasets
datasets download genome accession –inputfile accessions.txt –include gff3,gbff,rna,cds,protein,genome,seq-report Or you simply specify mutliple accessions on the commandline: datasets download genome accession GCF_000001405.40 GCA_003774525.2 GCA_000001635 Edit: Sorry, I overlooked the –inputfile option. This is necessary unless all accessions are from a common taxon or bioproject. In the first case you can…
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…
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…
Phylogenetic tree for my bins with abundance, genome size etc
I would like to create a tree for my MAGs/Bins like the image shown below. Can anyone please share me the steps/scripts in detail? When I used, gtdbtk de_novo_wf to analyze a set of bin files with -skip_gtdb_refs. I always ends up with the following error. [2023-11-20 12:55:35] INFO: Read…
Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization
Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….
HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases
HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…
txid1492[Organism:exp] AND “sequence from type”[Filter] – Assembly
Filters activated: Latest, Exclude anomalous. Clear all to show 4 items. Select item 78466111. ASM1413179v1 Organism: Clostridium butyricum (firmicutes) Infraspecific name: Strain: DSM 10702 Submitter: Helmholtz Centre for Environmental Research – UFZ Date: 2020/08/10 Assembly level: Complete Genome Genome representation: full Relation to type material: assembly from type material GenBank…
txid10366[Organism:noexp] – Assembly – NCBI
Taxonomy Murid betaherpesvirus 1 Murine cytomegalovirus (Murid betaherpesvirus 1) is a below-species classification of Muromegalovirus muridbeta1 Taxonomy ID: 10366 Source: KnownItemSensor Filters activated: Latest, Exclude anomalous. Clear all to show 15 items. Select item 141999781. ASM879276v1 Organism: Murid betaherpesvirus 1 (Murine cytomegalovirus) Submitter: na Date: 2023/05/04 Assembly level: Complete Genome…
Mapping .fna reference genome to itself in order to include it as an outgroup
Mapping .fna reference genome to itself in order to include it as an outgroup 0 Hello, Please pardon a potentially naive question. I have 30 newly sequenced WGS data files for a bird species.These are all in a FASTQ format. I have mapped them to a reference genome from NCBI,…
Unique names issue – mothur
hpmm75 October 18, 2023, 2:23pm 1 Please advise what to do with this error. I was running unique.seqs(fasta=full.trim.contigs.good.unique.good.filter.fasta, count= full.trim.contigs.good.unique.good.filter.fasta) in batch mode and I get this message below. unique.seqs(fasta=full.trim.contigs.good.unique.good.filter.fasta, count= full.trim.contigs.good.unique.good.filter.fasta) [ERROR]: Your count table contains a sequence named T—GC—GT-AG-GAG—–GCA-A-G–C–G–T–T–GT-C-CGG-AG—TT-A–C-T–GG-GC–GT–A—AA-GC-GT-GT—G-TA-G-G-C-G–G–T-GC-G-A-T—-GC–G-T-C-C——-G-G-T–G–TG–A-AA-TC–T-C-CC-G-G——-CT-T-AC–C-T-G-G-G-A-G–G-G—G-G–C-A–T–C——–G–GA-T-A—C——G–G-T–CA–C-A-C——-T-T-G-A-G-G–G—–C-AT——CA-G-A—-G-G-C-C—AG-T—–AG-A–ACT—C-C-C-G-GT–GG-A-C-CA-GT-G–A–A-A—TG-G-GT-AG–AG-A-TC–G-G-G-A-A-G-A-AT-A-CC—–AG–T–G–GT-GCA-G–A-C–G——-G–C-T-G-G—CTG—G–GG-T-G——————–T-A–C-C-T–GA–CG-C-T-G-A-GA-C-A-CG-A–AA-G-C–A-TG–GG-G–AG-C-A-AA———CA–GG-AT with a total=0. Please correct. [ERROR]: Your count table…
BIOT645 Week 7 Assignment .docx – 1 BIOT 645 Tocilizumab Week 7 Assignment Enzymes and Antibodies: Tocilizumab Natalie Figueroa Jones University of
2 BIOT 645Tocilizumab Drug/Biologic Tocilizumab (TCZ), also called Actemra, is a recombinant humanized anti-interleukin-6 receptor (IL-6R) monoclonal antibody. Currently, this drug is indicated for treating adults with moderate to severe rheumatoid arthritis (RA), giant cell arteritis (GCA), systemic sclerosis-associated interstitial lung disease (SSc-ILD), and cytokine release syndrome (CRS), as well…
USER_PROJECT_DENIED error calling Vertex AI from a Firebase Cloud Function with Python SDK
I am trying to load text-bison@001 model from a Firebase Cloud Function using Vertex AI SDK. from firebase_admin import initialize_app, firestore, storage, credentials import openai import os import stripe import vertexai from vertexai.language_models import TextGenerationModel def init_app(): cred = credentials.Certificate(“./serviceAccountKey.json”) initialize_app(cred) vertexai.init(project=”myapp”, location=”us-central1″) model = TextGenerationModel.from_pretrained(“text-bison@001”) return model However, I…
IJMS | Free Full-Text | Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761
1. Introduction The alarming decline of biodiversity worldwide necessitates urgent conservation measures, particularly for wild, endangered, and understudied species. According to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, of the 5973 mammal species assessed, 1340 were classified as threatened with extinction, including 233 critically…
The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons
The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…
Environment and taxonomy shape the genomic signature of prokaryotic extremophiles
Supervised machine learning analysis of the Temperature Dataset and the pH Dataset Supervised classification by taxonomy, environment category, and random label assignment Several supervised machine learning computational tests were performed to classify the Temperature Dataset and the pH Dataset, respectively, using (1) taxonomy labels (domain), (2) environment category labels, and…
Elusive syntax error in Snakefile
Elusive syntax error in Snakefile 0 Hi, I’m quite new to snakemake and was trying to write a little workflow to analyze some nanopore data. However, it keeps returning an invalid syntax error caused by this rule rule alignment: input: “{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz” output: “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam”, “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai” resources: partition: “EPYC” runtime: 5760 mem_mb:…
ncRNA | Free Full-Text | Long Non-Coding RNA TUG1 Gene Polymorphism and TUG1 Expression Level as Molecular Biomarkers of Systemic Lupus Erythematosus and Lupus Nephritis
1. Introduction Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a wide variety of manifestations ranging from mild cutaneous to organ failure as lupus nephritis (LN) and cardiopulmonary complications [1]. SLE is mainly present among young women, with a greater incidence in certain ethnic groups, such as Asian,…
The genomic footprint of whaling and isolation in fin whale populations
Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…
Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress
Bacterial isolation from Antarctic soil Soil samples were collected from the Cape Burk area (1: 74° 45′ 19.6″ S, 136° 48′ 44.6″ W)51. The soil (1 g) was inoculated in a Reasoner’s 2A (R2A) liquid (composed of 0.5% proteose peptone, 0.05% casamino acid, 0.05% yeast extract, 0.05% dextrose, 0.05% soluble starch,…
Problem with Mageck paired analysis
Problem with Mageck paired analysis 0 Dear all, I have a matter to submit. I’m trying to do a paired analysis, however, I’m getting this error. Error: incorrect number of dimensions in line 2 (16) compared with the header line (4). Please double-check your read count table file. This is…
The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data
Sample collection and DNA extraction An individual E. imbricata was obtained from the sea turtle rescue base on Naozhou Island, Zhanjiang City, Guangdong Province, China. A 10 mL blood sample was drawn from its jugular sinus and rapidly frozen for further analysis. Genomic DNA was extracted from the processed blood samples…
Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions
Reactor performance revealed temporal changes in propionate degradation rate The four propionate- and acetate-fed reactors used in the study produced biogas with an average methane content of 62–70% (Table S2). The pH was 8.1–8.3, resulting in an ammonia-nitrogen level of 0.7–0.9 g NH3 L-1. This free ammonia level is well above…
Finding the raw data used to build reference genomes
Finding the raw data used to build reference genomes 1 Is the a way to find the raw data (fastq or other) that was used to generate a reference genome? and is there a quick way to do this for a large number of genomes? reference-genome • 53 views •…
ASM170840v1 – Assembly – CNGBdb
Home Assembly GCA_001708405.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_001708405.1 ) 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…
IJMS | Free Full-Text | The Impact of the CYP2D6 and CYP1A2 Gene Polymorphisms on Response to Duloxetine in Patients with Major Depression
Received: 16 July 2023 / Revised: 25 August 2023 / Accepted: 29 August 2023 / Published: 30 August 2023 Round 1 Reviewer 1 Report The manuscript “The impact of the CYP2D6 and CYP1A2 Gene Polymorphisms on Response to Duloxetine in Patients with Major Depression” addresses how some SNPs of these…
ASM307627v1 – Assembly – CNGBdb
Home Assembly GCA_003076275.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_003076275.1 ) 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…
Characterization and comparative analysis of the Escherichia marmotae M-12 isolate from bank vole (Myodes glareolus)
Isolation and identification of E. marmotae M-12 The M-12 isolate was obtained from the lungs of a male bank vole (Myodes glareolus). Culture M-12 was stored in NB with 15% glycerol at − 80 °C. Microscopy investigation revealed a single Gram-negative coccobacillus in M-12 isolate. Catalase-positive and oxidase-negative reactions were observed. Isolate…
CircRNA-CIRH1A Promotes the Development of Osteosarcoma by Regulating PI3K/AKT and JAK2/STAT3 Signaling Pathways
Tissue Collection The study was approved by the Medical Ethics Committee at the Fuyang Traditional Chinese Medicine Orthopedics Hospital (2019-F027). OS tumor tissues and adjacent normal tissues were collected from 40 patients diagnosed with OS at the Fuyang Traditional Chinese Medicine Orthopedics Hospital from June 2018 to Dec 2019. Patient…
ASM638587v1 – Assembly – CNGBdb
Home Assembly GCA_006385875.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_006385875.1 ) 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…
Multidrug-resistant Providencia rettgeri strain YQ150713.
Introduction Providencia rettgeri is a Gram-negative opportunistic human pathogenic bacterium that belongs to the Proteae bacteria. It is a pathogen commonly found in the hospitals that mainly cause urinary tract infections, pneumonia, bacteremia, neonatal sepsis, eye infections, meningitis, endocarditis, and diarrhea.1–3 The pathogen Providencia rettgeri demonstrates inherent resistance to numerous…
ASM141870v1 – Assembly – CNGBdb
Home Assembly GCA_001418705.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_001418705.1 ) 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…
Annotating Chr level assembly using Scaffold level Ref. Assembly
Genome Annotation : Annotating Chr level assembly using Scaffold level Ref. Assembly 0 Hi All, Currently, I am trying to annotate a chromosome-level assembly (GCA_029169275.1) using the scaffold-level reference assembly (GCF_001442555.1). I already annotated the assembly using MOSGA pipeline (Augustus). If needed, I can also use the Geneious annotation pipeline….
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Genome assembly, annotation, and overview We assembled a chromosome-scale genome of a GS E. indica plant using PacBio Sequel II and long-range interaction (Hi-C) datasets. The assembly consists of nine chromosomes spanning 509,878,742 base pairs estimated to be ~97.8% complete by Benchmarking Universal Single-Copy Orthologs (BUSCO)28 analysis with an LTR…
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…
Internal error (code 13) when tuning a model in Ve…
When processing a model tuning in Vertex AI, during the pipeline creation, i recieved an Internal error message.: INFO:google.cloud.aiplatform.pipeline_jobs:PipelineJob projects/xxxxxxxxx/locations/xxxxx-xxxxx/pipelineJobs/tune-large-model-xxxxxxxxxxx current state: PipelineState.PIPELINE_STATE_PENDING ————————————————————————— RuntimeError Traceback (most recent call last) <ipython-input-5-591a9a561b04> in <cell line: 4>() 2 vertexai.init(project=”xxxxxxxxx”, location=”us-central1″) 3 model = TextGenerationModel.from_pretrained(“text-bison@001”) —-> 4 model.tune_model( 5 training_data=training_data, 6 train_steps=100, 3…
Reference genome for oryza sativa indica group
Ensembl Oryza sativa indica genome was submitted by Beijing Genomics Institute: www.ebi.ac.uk/ena/browser/view/GCA_000004655.2 If the MSU genome came from the same submission then they should be identical. There are a total of 25 indica genomes available in NCBI www.ncbi.nlm.nih.gov/datasets/genome/?taxon=39946 but out of the lot one referred to above seems to be…
2023-07-24 | NYSE:ABBV | Press Release
– First registered, randomized Phase 3 trial in hidradenitis suppurativa (HS) evaluating the efficacy and safety of upadacitinib (RINVOQ®) in adults and adolescents with moderate to severe HS1 – HS is a difficult-to-treat chronic, inflammatory disease with few therapeutic options available2,3 – AbbVie applies proven expertise in immunology and HS…
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…
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…
theta parameter file was not given
Strelka error: theta parameter file was not given 0 Hi guys, I’m trying to run strelka2 somatic workflow on my matched normal-tumor samples, but I keep running into the following error: [TaskManager] Launching command task: ‘CallGenome+callGenomeSegment_chromId_002_chr3_0015’ from sub-workflow ‘CallGenome’ [TaskRunner:CallGenome+callGenomeSegment_chromId_002_chr3_0015] Task initiated on local node [TaskManager] [ERROR] Failed to complete…
ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis
Bacterial strains and culture conditions Escherichia coli strain DH5α (Thermo Fisher) was used for the propagation of plasmids, whereas E. coli BL21 DE3 (Novagen) was used for the expression and purification of ResR/McdR protein. Mtb Erdman was obtained from Dr. Ramandeep Singh at THSTI, India, and Mtb H37Rv mc2 790242…
adding features to gtf file using agat tool function
I m trying to use this agat which adds new attributes from tsv to gtf file. My file formats are as such input tsv which is my reference file gene_id Entrez_ID ENSCAFG00845006432 399518 ENSCAFG00845002136 399530 ENSCAFG00845029798 399544 ENSCAFG00845011460 399545 ENSCAFG00845001610 399653 ENSCAFG00845013158 403157 ENSCAFG00845014982 403168 ENSCAFG00845021967 403170 ENSCAFG00845019241 40340 Next…
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…
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]
Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…
Index of /goldenPath/hg38/vsGCF_012559485.2
Index of /goldenPath/hg38/vsGCF_012559485.2 This directory contains alignments of the following assemblies: – target/reference: Human (hg38, Dec. 2013 (GRCh38/hg38), GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) – query: crab-eating macaque (GCF_012559485.2_MFA1912RKSv2, 2021-10-26, Keio University / RIKEN) Files included in this directory: – md5sum.txt: md5sum checksums for the files in this…
rna seq – building custom gtf file with entrez ID for any organism
How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf. My organism is canis_familaris I have to use is this source. How do I…
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…
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…
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…
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…
NCBI Genome Download Sequence Report Indexing Sequences FNA file Tool Exist?
Forum:NCBI Genome Download Sequence Report Indexing Sequences FNA file Tool Exist? 0 I’m looking to find an optimal global alignment for a coral genome to other mRNA sequences in other organisms. I pressed the download button to get the genome sequences(FASTA), Sequence Report(JSONL), and Assembly data report (JSONL). When it…
Extract compounds/proteins from genomic data
Extract compounds/proteins from genomic data 0 Hello, First of all, sorry for this noobish question and secondly, I posted the same question on StackExchange but I don’t think it will get any answer there (low traffic, the question got closed as “not bioinformatics”). I’m wondering, if, by bioinformatic means only,…
Using TRF in multiple files
Using TRF in multiple files 0 Hi there guys. I would like to run trf in a lot of fasta files, however, when I tried this simple loop: #! usr/bin/env bash # Genomes_new/Bacteria/Pseudomonadota/Acidithiobacillia for fasta in /Genomes_new/Bacteria/Pseudomonadota/Acidithiobacillia/CHR/*_chr.fna; do trf “$fasta” 2 7 7 80 10 50 500 -h done It…
acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens
acCRISPR framework acCRISPR performs essential gene identification by calculating two scores for each sgRNA, namely the cutting score (CS) and the fitness score (FS). CS and FS are the log2-fold change of sgRNA abundance in the appropriate treatment sample with respect to that in the corresponding control sample (see Supplementary…
Getting species names and taxa id from assembly accession number
Hi folks! I have a list of NCBI assembly accession numbers, and I’m trying to return species name (latin and common) plus taxid. A few weeks ago, I wrote a bit of code that appeared to do the trick. #!/usr/bin/env python import csv from Bio import Entrez Entrez.email=”kwh1@wi.mit.edu” def get_organism_taxonomy(accession):…
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…
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…
python – Missing markers in the plot legends of scikit-learn examples
This question already has answers here: Closed 1 hour ago. I have been looking at the Scikit library documentation and example codes. Many of the plots does not have markers in the legends, leaving us to guess everything. Example code : import matplotlib.pyplot as plt from…
DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals | BMC Genomic Data
Demographics Data from three studies were included: Dan-NICAD: 1,649 individuals with symptoms of obstructive coronary artery disease, predominantly chest pain, undergoing coronary computed tomography angiography. In total, 52% were females, the mean age was 57 years (+/- 9 SD), median coronary artery calcium score were 0 [0–82] and 24% of…
2023-05-25 | NYSE:ABBV | Press Release
NORTH CHICAGO, Ill., May 25, 2023 /PRNewswire/ — AbbVie (NYSE: ABBV) today announced the New England Journal of Medicine (NEJM) published results from the pivotal Phase 3 clinical trials – U-EXCEL, U-EXCEED and U-ENDURE – evaluating upadacitinib (RINVOQ®) in adult patients with moderately to severely active Crohn’s disease who have…
PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum
Despite being an established model, the genome and annotation of P. tricornutum are not concordant and the existing epigenetic resources generated so far lack a well-defined framework for accurate and user friendly utilization. To address this limitation, we sought to establish a coherent resource rendering the multiple genomic and epigenomic…
Deletion of endothelial leptin receptors in mice promotes diet-induced obesity
Experimental animals The generation of mice with tamoxifen-inducible, Tie2.Cre-ERT2-mediated deletion of LepR in endothelial cells was described previously12,17. For Cre recombinase activation, mice (6 weeks-of-age) were fed tamoxifen citrate-containing rodent chow (Envigo; TD.130860) for 6 weeks49. Genomic DNA from the brain, lung, small intestine, subcutaneous adipose tissue (SCAT) and visceral adipose tissue…
Reconstruction of the personal information from human genome reads in gut metagenome sequencing data –
Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…
Reconstruction of the personal information from human genome reads in gut metagenome sequencing data
Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…
Mosquito densovirus significantly reduces the vector susceptibility to dengue virus serotype 2 in Aedes albopictus mosquitoes (Diptera: Culicidae) | Infectious Diseases of Poverty
Identification of MDV presence using open access sequencing data Metagenomic next-generation sequencing (NGS) data for field mosquitoes in China were searched from the NCBI SRA database (www.ncbi.nlm.nih.gov/sra) and CNGB Sequence Archive database (db.cngb.org/cnsa/) using the keywords “mosquito OR Anopheles OR Aedes OR Culex”. Followed by removing the datasets with less…
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Figure 1 shows the detailed workflow of the study. Fig. 1 General overview of the study. Briefly, MPXV was isolated from a skin lesion and then was used to infect CV-1 cells. After the designated infection times, total RNA was isolated and sequenced using direct cDNA sequencing protocol on ONT’s MinION platform….
Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage
1. Introduction Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella, which affects domestic livestock and a wide range of wild mammals (Ducrotoy et al., 2017). The disease is amongst the most common zoonotic infections globally, with an estimated 500,000 human cases annually (Pappas et al., 2006),…
Research Associate/Senior Research Associate in Bioinformatics at Newcastle University
We are a world class research-intensive university. We deliver teaching and learning of the highest quality. We play a leading role in economic, social and cultural development of the North East of England. Attracting and retaining high-calibre people is fundamental to our continued success. The RoleThis new position is a…
RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation
Cell strains E. coli DH5α and B. subtilis 168 strains were grown overnight in Luria-Bertani broth at 37 °C and 180 rpm to a final OD600 ~1.7. B. subtilis strain 168 was kindly provided by Dr. S.A. Dubiley (Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia). T. adornatum strain…
Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study | Infectious Diseases of Poverty
Epidemic profile of Yersinia during 2007–2019 A total of 9031 samples were monitored from 2007 to 2019, with the detection rate of Yersinia ranging from 0.9% to 7.6% (Table 1). The highest detection rate was in 2014 (7.6%), eightfold higher than in 2013 (0.5%). The difference in positivity rates between…
error_in _running_RepeatModeler
error_in _running_RepeatModeler 0 I was running RepeatModeler and got the error as follows : RepeatModeler -engine ncbi -database GCA_902806645.1_cgigas_uk_roslin_v1_genomic RepeatModeler Version open-1.0.8 ================================ Search Engine = ncbi Database = GCA_902806645.1_cgigas_uk_roslin_v1_genomic . – Sequences = 236 – Bases = 647887097 Using output directory = /mnt/g/manaswini/transib_ancenstry/18th_april_2023_rag2/mollusca/Crassostrea gigas/repeat_modler/RM_2100.TueApr181550582023 RepeatModeler Round # 1 ========================…
Download many NCBI genomes with list of GCA identifiers
Download many NCBI genomes with list of GCA identifiers 1 Hi, I have a list of NCBI GCA/GCF identifiers for many (hundreds of) vertebrate whole genomes that I would like to download. I initially tried Entrez.efetch, but have realized GCA numbers cannot be used with it, and this also may…
MoritellaJT01 – Assembly – CNGBdb
Home Assembly GCA_001574435.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_001574435.1 ) 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…
Index of /goldenPath/hg38/vsTurTru2
Index of /goldenPath/hg38/vsTurTru2 This directory contains alignments of the following assemblies: – target/reference: Human (hg38, Dec. 2013 (GRCh38/hg38), GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) – query: Dolphin (turTru2, Oct. 2011 (Baylor Ttru_1.4/turTru2), Baylor College of Medicine Ttru_1.4 (NCBI project 20365, GCA_000151865.2, WGS ABRN02)) Files included in this directory:…
Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past
Two new Tepidiforma species expand on a small number of cultivated Dehalococcoidia Two bacterial strains were isolated from terrestrial geothermal springs by plating benthic mat and sediment slurries onto R2A medium and were identified by 16S rRNA gene sequencing as members of the recently described genus Tepidiforma [27]. Strain YIM…
PhiSpy Predictions in GenBank Format
This file has GenBank format flat files for all the prophage regions we identified. The GenBank files are essentially a slice of all the data from the genome annotation. We added a few PhiSpy-specific outputs, like hits to VOGdb proteins and the E-value of those matches. We searched everything against…
Any way to retrieve the annotation information of genomes under a bioproject ? (NCBI)
Any way to retrieve the annotation information of genomes under a bioproject ? (NCBI) 1 Hello! I want to retrieve the annotation data (tRNAs, rRNA genes) from genomes located under this bioproject www.ncbi.nlm.nih.gov/bioproject/729490 There are 677 genomes and by clicking on the “Genome-Annotaiton-Data” of each genome entry (e.g GCA_029245675.1) I…
sorting and moving a bunch of fasta files into separate folder
sorting and moving a bunch of fasta files into separate folder 1 Hi guys, I have 1000s of MAGs fasta files in a single folder. So I wanted to move only a few groups of MAGs into a separate folder. So I have listed all the files ( eg. GCA_003221885.fa)…
Chromosome-level genome assembly of the critically endangered Baer’s pochard (Aythya baeri)
Ethics statement All animal handling and experimental procedures were approved by the Qufu Normal University Biomedical Ethics Committee (approval number: 2022001). Sample and sequencing Baer’s pochard tissue for whole-genome sequencing was obtained from a dead individual that had strayed into a fishing net in Shandong (China). The muscle tissue that…
Dealing with “Too many samples were discarded” – StrainPhlAn
I’m attempting to do a strainphlan analysis of Blautia wexlerae, but nothing I’m doing is working. I think the problem might be the reference genomes that I’m using, but I’m using the 2 primary genomes from NCBI. Is there another place to get correctly formatted references? Error Here’s the primary…
ASM317379v1 – Assembly – CNGBdb
Home Assembly GCA_003173795.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_003173795.1 ) 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…
known-sites for Felis_catus_9.0 (GCA_000181335.4)
known-sites for Felis_catus_9.0 (GCA_000181335.4) 1 Good afternoon dear members, I am processing Cat WGS samples and running gatk BaseRecalibrator and one of the required parameters is –known-sites – One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. Does anyone know where I…
Full-length human dystrophin on human artificial chromosome compensates for mouse dystrophin deficiency in a Duchenne muscular dystrophy mouse model
Ethics declarations This study was approved by the Animal Care and Use Committee of Tottori University (Permit Number: 16-Y-20, 17-Y-28, 19-Y-22, 20-Y-31, 21-Y-26, and 22-Y-36). All experiments were carried out in compliance with the ARRIVE guidelines. All methods were performed in accordance with the relevant guidelines and regulations. Mice were…
featureCounts with NCBI T2T not capturing all genes
Hello, My team would greatly appreciate assistance with running featureCounts using the human NCBI T2T assembly (assembly (T2T-CHM13v2.0) as a reference; when we run it we end up with nearly 14,000 fewer genes than what the annotation supposedly contains.What (if any) modifications can be made to run Subread or RSubread…
Strain-level bacterial typing directly from patient samples using optical DNA mapping
Figure 1a provides an overview of the experimental procedure and it is summarized in the following sections. Fig. 1: Schematic overview of high-resolution optical DNA mapping-based bacterial typing. a Experimental pipeline. The DNA, extracted via plug-lysis, is labelled with YOYO-1 and netropsin in a single step. The DNA is confined to…
Getting a curl: (22) The requested URL returned error: 500 ERROR
Getting a curl: (22) The requested URL returned error: 500 ERROR 0 Hi dear friends I am trying to use a list of assemblies (one by line) to download some data from ncbi. Example of the list: GCA_937921735.1 GCA_937897655.1 GCA_902386345.1 GCA_902386385.1 GCA_902386595.1 I am using this command (that I think…
Identification of an unrecognized circRNA associated with development of renal fibrosis
Front Genet. 2022; 13: 964840. , 1 , 1 , 1 , 2 , 2 , 2 , 2 , 2 , 3 ,* and 4 ,* Yun Zhu 1 Department of Dermatology, The People’s Hospital of Yuxi City, Yuxi, China Weimin Yan 1 Department of Dermatology, The People’s Hospital…
Python 01 in Bioinformatics | Processing Gene Sequences from Scratch
1. Download of sequence data When we start to understand the processing flow of the sequence, we first need to know the sequence download URL. One of the well-known websites is NCBI (National Center for Biotechnology Information) US National Center for Biotechnology Information. 1. Enter NCBI through the following website,…
A 10-year microbiological study of Pseudomonas aeruginosa strains revealed the circulation of populations resistant to both carbapenems and quaternary ammonium compounds
P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…
Can’t liftover vcf file from hg19 to hg38
Can’t liftover vcf file from hg19 to hg38 1 Hello everyone I have a vcf file that I’m trying to convert from hg19 to hg38. For that I’m using bcftools +liftover command from here . I previously tried to use picard VCF but the memory cost was too much from…
Molecular characterization and antimicrobial susceptibility profiles of Thai Mycoplasma synoviae isolates
Isolation of M. synoviae field isolates M. synoviae field isolates were obtained from approximately ninety flocks of registered commercial chicken farms, including breeder flocks, broiler flocks, and layer flocks in Thailand in 2020. Chickens were individually swabbed at the articular joint or the respiratory tract; choanal cleft, tra,chea and airsac;…
Cost-effective and accurate genomics analysis with Sentieon on AWS
This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…
Too many positional arguments (1))
blastn (Error: Too many positional arguments (1)) 1 Hello, I want to use blastn to search a particular query in the fasta format ($QUERY) I’ve created database from each .fna file using `”makeblastdb -in $GENOME -dbtype nucl -parse_seqids” (for different purposes, I run also blastcmd which runs normally without any…
pandas – Logistic Regression with scikit-learn giving key error while printing output as : KeyError: ‘Logistic Regression’
plt.figure(figsize = (12,7)) ax = sns.barplot(x = models,y = accuracy_list) plt.xlabel(“Classifiers”,fontsize = 15) plt.ylabel(“Accuracy (%)”, fontsize =15) for p in ax.patches: width = p.get_width() height = p.get_height() x= p.get_x() y = p.get_y() ax.annotate(f”{height} %”,(x + width/2 , y + height*1.01),ha = “center”) plt.show() while i’m runing the above code i…