Tag: ENA

Talentify helps candidates around the world to discover and stay focused on the jobs they want until they can complete a full application in the hiring company career page/ATS. Seeking a Bioinformatics Analyst 100% Remote Description Support of computational research priorities associated with oncology discovery programs. This variably entails querying…

How to deal with SRA file without .SRA 0 Good afternoon, I have encountered a problem with an SRA file and I hope you can help me. I downloaded the SRA file from this website: www.ebi.ac.uk/ena/browser/view/PRJNA834732. I obtained the SRA file without the .SRA extension. I used fast-dump to extract…

Title: Bioinformatics Analyst III Duration: 12 Months Location/Site: 100% Remote Pay Rate: $51/hr. – $56/hr. on w2 Job Description Services Overview: Services include support of computational research priorities associated with oncology discovery programs. This variably entails querying public cancer genomics resources for mutation/expression distributions, assessing normal expression, interpreting germline associations…

job summary: As the largest staffing and recruitment agency in the world, we can commit to finding you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network of…

We are looking to hire a capable Bioinformatics Analyst to join our passionate team at Synectics Inc in North Chicago, IL.Growing your career as a Full Time Bioinformatics Analyst is a terrific opportunity to develop relevant skills.If you are strong in planning, problem-solving and have the right experience for the…

Remote role Title – Bioinformatics Analyst We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should be familiar with developing…

Remote role Title – Bioinformatics Analyst We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should be familiar with developing…

Title – Bioinformatics AnalystTypically between 9 AM-5 PM Central Time.Remote We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should…

Carlson, J. L., Erickson, J. M., Lloyd, B. B. & Slavin, J. L. Health effects and sources of prebiotic dietary fiber. Curr. Dev. Nutr. 2, nzy005 (2018). Article  PubMed  PubMed Central  Google Scholar  Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid…

Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

Nucleotide databases are repositories that store and provide access to nucleotide sequence data. These databases contain a vast collection of DNA and RNA sequences from various organisms, including viruses, bacteria, plants, animals, and humans. Nucleotide databases play a crucial role in genomics, molecular biology, and bioinformatics research by providing a…

2 hours ago Article URL: www.ncbi.nlm.nih.gov/genbank/ Comments URL: news.ycombinator.com/item?id=36038722 Points: 1 # Comments: 0 GenBank OverviewWhat is GenBank?GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which…

This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can check the corresponding alive record for U49845, and seeexamples of other records the show a range of biological features. SITE SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene,…

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….

Issue about generating EMBL Flat file for ENA submission 0 Hello all! I am trying to generate an EMBL flat file to submit an annotated assembly to ENA. I am using EMBLmyGFF3 to generate the flat file from the whole genome FASTA file and the GFF3 file. I am getting…

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),…

During the COVID-19 pandemic, one online platform emerged as the main repository for viral genome data. GISAID, an initiative launched in 2008 to improve the global sharing of influenza data, earned the trust of scientists by ensuring that they would be credited for the data they generated. It now hosts…

Bergqvist, C. et al. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J. Rare Dis. 15, 1–23 (2020). Article  Google Scholar  Martin, G. A. et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell 63, 843–849 (1990)….

Issue With CRAM -> BAM -> FASTQ Conversion 2 Please help! I am trying to obtain fastq files from the GDSC, all we have in the lab is CRAM files. Unfortunately, the reference genome seems to not exist when pulled from an online source. I have attempted to use the…

curl -s “https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks?format=json” | jq ‘.'{ “version”: “6.8”, “hitCount”: 9, “request”: { “id”: “33024307”, “source”: “MED” }, “dataLinkList”: { “Category”: [ { “Name”: “Nucleotide Sequences”, “CategoryLinkCount”: 5, “Section”: [ { “ObtainedBy”: “tm_accession”, “Tags”: [ “supporting_data” ], “SectionLinkCount”: 5, “Linklist”: { “Link”: [ { “ObtainedBy”: “tm_accession”, “PublicationDate”: “04-11-2022”, “LinkProvider”: { “Name”:…

Creating a reference panel of equus caballus sequences 1 Hi all, I have a quick question regarding the starting of my masters project that I’m trying to understand, I am currently trying to create a reference panel of wgs for the species equus caballus (horse) as part of my research…

The impact of X overdosage on the global transcriptomes of Saudi and ENA KS-iPSCs. A) Venn diagram showing the DEGs shared in the contrast 47,XXY Vs. 46,XY in iPSCs generated from ENA and Saudi KS patients. B) Gene Ontology analysis on common DEGs using the GO enriched for Biological Processes…

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…

We release metagenomic data of seven urban, eutrophic Swedish lakes that have been extensively studied and characterized in terms of biogeochemistry. Here we provide the supplementary tables and the full set of metagenome-assembled genomes of 17 metagenomic samples. – We have 10 metagenomic samples from Lake Mälaren which is the…

Introduction Colorectal cancer (CRC) is a leading cause of cancer-related death1 and its mortality rate is expected to rise worldwide, due to population growth and aging, thus entailing a global public health challenge. CRC mortality is mainly due to therapy resistance and metastasis, which are driven by a small population…

Obtain number of base pairs in a genome 1 HI! It’s going to be a stupid question since I’m not anyhow related to bioinformatics – I’m interested into how can I obtain the number of base pairs in my genome sample. I’m trying to remake the experiment that was made…

Let me show you an example: trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR16093385&display=metadata This data contains two reads, R1 and R2. The read length of R1 and R2 are the same 150bp. However, this experiment is performed following 10x 3’library protocol. In the method section, it described as below: The scRNA-seq libraries were generated using the…

Ensuring open data from landmark biodiversity projects and smaller genome sequencing initiatives are readily-available to the global scientific community Genomic data for biodiversity research is produced and shared worldwide. Credit: Karen Arnott/EMBL-EBI As major biodiversity projects increasingly use genomic sequencing to catalogue and understand species, EMBL-EBI is ensuring that the…

Error while converting GFF file to GTF using AGAT 0 Hi I am trying to convert a gff file to gtf file which I want to use for STAR. I tried AGAT(latest version) to convet but it gives me a series of error(mailny tow types) .I have attached the error…

Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…

Hi, I am new to Single cell analysis but have some experience with NGS data output and manipulation. I have a set of .bam that I assume were the product of the cell ranger pipeline from the ENA (project ID PRJEB36998) unfortunately I have no access to any other output…

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…

Alignment in bioinformatics 1 my project talk about gene expression profile of Mycobacterium tuberculosis on lung , i choose my samples from ENA :www.ebi.ac.uk/ena/browser/view/PRJEB19976 , I download reference genome from NCBI : www.ncbi.nlm.nih.gov/genome/?term=h37rvand , I create an index by myself using HISAT2 and after that i started the process of…

NEW YORK – The Institut Pasteur in Paris has won €2 million ($2.1 million) in EU funding to create a “search engine for DNA sequencing data,” indexing next-generation sequencing data available in the Sequence Read Archive in order to make it searchable and more accessible. The five-year IndexThePlanet project, led…

Tellus Solutions is in partnership with a committed biopharmaceutical company in North Chicago focused on providing innovative therapies. Your technical expertise as a Bioinformatics analyst in the area of using R to do basic data analysis (processing, plotting), RNA-Seq alignment experience will contribute to our client’s innovative therapies which will…

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

WALTHAM, Mass. and BOULDER, Colo., Oct. 26, 2022 (GLOBE NEWSWIRE) — Cogent Biosciences, Inc. (Nasdaq: COGT), a biotechnology company focused on developing precision therapies for genetically defined diseases, today announced that it will be presenting two preclinical posters at the EORTC-NCI-AACR (“ENA”) annual meeting to be held October 26-28, 2022. Presentations…

Job description Tellus Solutions is in partnership with a committed biopharmaceutical company in North Chicago focused on providing innovative therapies. Your technical expertise as a Bioinformatics analyst in the area of using R to do basic data analysis (processing, plotting), RNA-Seq alignment experience will contribute to our client’s innovative therapies…

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

Hi, all! I download fastq.gz files of GSE162708 from ENA which only have 2 files of each sample(usually scRNA-seq has 3 files I1 , R1 & R2 ). Then I run fastp as following Then I get QC report , but I can’t understand why Per base sequence content of…

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

A worldwide consortium of scientists, led by the Earlham Institute and the University of Liverpool, has developed an efficient, inexpensive approach to large-scale bacterial genome sequencing that could equip researchers in low- and middle-income countries (LMICs) with cheap and accessible methods for sequencing large collections of bacterial pathogens—at a cost…

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

These datasets reuse the globally comprehensive DNA sequence data that ENA and its partners, the National Centre for Biotechnology Information (NCBI)  and the DNA Data Bank of Japan, maintain in the International Nucleotide Sequence Database Collaboration (INSDC). EMBL-EBI maintains ENA, which supplied the first DNA-derived dataset shared through GBIF in…

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

The faces of three ancient Egyptians are brought back to life thanks to DNA group of scientists Recreate The faces of three ancient Egyptian men using DNA that is more than 2,000 years old. According to the magazine NEWSWEEKIt is believed that this is the first time that modern techniques…

The faces of three ancient Egyptian men have been brought to life by scientists, using DNA that is more than 2,000 years old. This is thought to be the first time modern techniques have been used on human DNA of this age, with the trio of samples estimated to be…

New Snapshot methods for low-coverage sequencing bring hidden data to life Scientific Poster Image Scientific Poster Image Scientific Poster Image RESTON, Va., Sept. 15, 2021 (GLOBE NEWSWIRE) — At the 32nd International Symposium on Human Identification (ISHI), being held this week in Orlando, Florida, Parabon NanoLabs will unveil for the…

I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp? 1 I downloaded sequencing files from 2 patients from here: www.ebi.ac.uk/ena/browser/view/PRJNA588461?show=reads there is one fastq file for the forward (1) and reverse (2) reads. I wanted to look…

project number: PRJNA505380 An example of Run accession: SRR8244780 Issue: Inconsistency between the library layout of Run and data source. As the library layout both in ENA and SRA labeled, Runs in Bioproject PRJNA505380 should be pair-end reads data. But some of them only have a single fastq and without…

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…