Tag: ncbi

minimap2, before or after assembly?

minimap2, before or after assembly? 1 Dear all, I feel confused because I saw someone uses the minimap2 after demultiplexing, but before proceeding with the assembly (CANU) [case 1], and someone using the minimap2/samfile/BFCTools/medaka after assembly (always CANU) [case 2]. In case 1, the reference file used to align against…

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Downloading genes from NCBI in fasta format

I’m pretty new in bioinformatics. I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I’d rather do this through via code than download each gene manually from the NCBI database. The genes belong to 2 different organisms (bacteria)…

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Compressing BAM, SAM, CRAM | Genozip

How good is Genozip at compressing BAM files? ​ See Benchmarks. ​ Compressing a BAM, SAM or CRAM file  ​ In the rest of this page we will give examples of BAM files. Genozip is also capable of compressing SAM files, and with some limitations, CRAM files as well. ​…

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genbank sequence format

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…

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EMDB < EMD-20433

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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Biochemical characterization of the two novel mgCas12a proteins from the human gut metagenome

Discovery of 11 new Cas12a candidates from a human gut microbiome database To discover new members of the Cas12a protein family, we built a pipeline that searches and sorts out new candidates from the National Center for Biotechnological Information (NCBI) human metagenome database. Using this search pipeline (Fig. 1a), we initially…

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Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

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Unexpected absence of ribosomal protein genes from metagenome-assembled genomes

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article  PubMed  Google Scholar  Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…

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Doubt on annotation of ensembl ids in biomart using R

Doubt on annotation of ensembl ids in biomart using R 0 Hi All 🙂 I have a large list of unique ENSEMBL IDs (48,432) representing mouse genes, my goal only is to get attributes like gene name and ncbi id to build a dataset with expression data. However when using…

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Bioinformatics Analyst II Job in Maryland (MD), Research and Development Career, Full Time Jobs in Frederick National Laboratory for Cancer Research

Bioinformatics Analyst II Job ID: req3154Employee Type: exempt full-timeDivision: Applied & Development Research ProgramFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical…

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How to retrieve all genes of interest from GenBank?

How to retrieve all genes of interest from GenBank? 1 Hello Bioinformagicians! My goal is to create a phylogenetic tree using mitochondria genes of ticks. I’ve recently use genes taken from Refseq complete genomes. However, I want to include gene sequences that may not be part of complete genomes. How…

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cell Large Granular Lymphocytic Leukemia

Large granular lymphocyte leukemia (LGLL) is a rare chronic lymphoproliferative disorder originating in the mature T-cells and natural killer (NK) cells, accounting for 2% to 5% of all the chronic lymphoproliferative disorders in North America and Europe. T-cell LGLL (T-LGLL) is the most common subtype representing about 85% of LGLL…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

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KEGG T00005: YNL036W

Entry YNL036W           CDS       T00005                                  Symbol NCE103, NCE3 Name (RefSeq) carbonate dehydratase NCE103   KO K01673   carbonic anhydrase [EC:4.2.1.1] Organism sce  Saccharomyces cerevisiae (budding yeast) Pathway sce00910   Nitrogen metabolism sce01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:sce00001] 09100 Metabolism  09102 Energy metabolism   00910 Nitrogen metabolism    YNL036W (NCE103)Enzymes [BR:sce01000] 4. Lyases  4.2  Carbon-oxygen lyases   4.2.1  Hydro-lyases    4.2.1.1  carbonic anhydrase     YNL036W (NCE103) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: …

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Nociceptor neurons affect cancer immunosurveillance

Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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Shared mechanisms and crosstalk of COVID-19 and osteoporosis via vitamin D

Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798), 270–273. doi.org/10.1038/s41586-020-2012-7 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Lipsitch, M., Swerdlow, D. L. & Finelli, L. Defining the epidemiology of Covid-19—Studies needed. N. Engl. J. Med. 382(13), 1194–1196. doi.org/10.1056/NEJMp2002125…

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Merging csv files with specific headers

Hello all, I have a directory with csv files (tab delimited). Each file have different sections (4 headers): miRDeep2 score novel miRNAs reported by miRDeep2 novel miRNAs, estimated false positives novel miRNAs, estimated true positives known miRNAs in species known miRNAs in data known miRNAs detected by miRDeep2 estimated signal-to-noise…

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Evasion of cGAS and TRIM5 defines pandemic HIV

Cells and reagents HEK293T and U87 cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Labtech) and 100 U ml−1 penicillin plus 100 μg ml−1 streptomycin (Pen/Strep; Gibco). THP-1-IFIT1 cells that had been modified to express Gaussia luciferase under the control of the IFIT1 promoter were described previously62. THP-1…

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advantages of electroporation

Therapeutic mRNAs can be stabilized by the incorporation of modified nucleosides, synthetic capping, and the addition of lengthy poly-A tails, and can be enhanced with codon optimization (1113). Maintains viability . Plant tissue culture is a collection of techniques used to maintain or grow plant cells, tissues or organs under…

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Bioinformatics tools and data retrieval

The Job Dispatcher service at the EMBL-EBI provides access to various sequence analysis tools and a database retrieval system (Dbfetch). This virtual course is split into two sessions running over two days.  During the first session, you will learn how to access and use our sequence…

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MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network | BMC Bioinformatics

Problem description Limited by time and cost, exploring the correlations between circRNAs and human diseases based on biological experiments has encountered many difficulties and bottlenecks. Instead of traditional experiments, computational methods are proved to be an efficient and accurate way to discover the potential connections between circRNAs and diseases. Data…

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Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Overview of the viromes In all, 41 wild Qinghai voles were collected from pasture habitats located on the eastern Tibetan Plateau, China (Fig. 1). Tissue samples from liver, lung, spleen, small intestine (with content), and feces (large intestinal content) of each vole were disrupted, and viral RNA was extracted. The RNA…

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NCBI/blast349 – WWW Error 404 Diagnostic

NCBI/blast349 – WWW Error 404 Diagnostic The page you requested ( h t t p : / / b l a s t . n c b i . n l m . n i h . g o v / b l a s t / B l a…

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Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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Bioinformatic Analyst job at Tellus Solutions in Remote

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…

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Number of sequences in RefSeq.

Number of sequences in RefSeq. 2 Dear colleagues I can not understand. When I download all the genomic sequences from the refseq database, after counting, I see that there are much fewer records than presented in the release (123394 organisms ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release214.txt). What am I doing wrong? 1. wget ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt 2….

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Building a Simulated Metagenomic Dataset

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

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Confrontation of AlphaFold models with experimental structures enlightens conformational dynamics supporting CYP102A1 functions

Prediction of alternate structures of CYP102A1 The competitive modelling approach was designed considering that the CYP102A1 FMNd must form alternate electron transfer complexes with the FADd and the P450d to support catalytic cycles, but that a direct electron transfer from FADd to P450d is not possible. In the dimeric structure…

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RefSeq release 214 is available! – NCBI Insights

RefSeq release 214 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in…

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Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

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Nasal Covid Vaccines To Be A Game-changer: Scientists

Share Tweet Share Share Email In mice, a prospective COVID-19 vaccination that is administered by the nose shows promise. One day you might only need to scent to protect yourself from COVID-19. Professors of radiology Ramasamy Paulmurugan and Tarik Massoud are leading an…

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Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious

Introduction Infection due to myelosuppression after chemotherapy for malignancies is a common complication and cause of treatment-related death.1,2 In clinical practice, the traditional identification of pathogens relies heavily on laboratory capacity to detect common pathogenic microorganisms with discrete methods, such as assays for pathogen-specific antibodies, nucleic acids and antigens, and…

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KEGG T01001: 4171

Entry 4171              CDS       T01001                                  Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2   KO K02540   DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa  Homo sapiens (human) Pathway hsa03030   DNA replication hsa04110   Cell cycle Disease H00604   Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing  09124…

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KEGG T02666: 101290786

Entry 101298727         CDS       T02666                                  Name (RefSeq) triacylglycerol lipase SDP1   KO K14674   TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve  Fragaria vesca (woodland strawberry) Pathway fve00100   Steroid biosynthesis fve00561   Glycerolipid metabolism fve00564   Glycerophospholipid metabolism fve00565   Ether lipid metabolism fve00590   Arachidonic acid metabolism fve00591   Linoleic…

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Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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Is Pulmonary Arterial Hypertension Risk Assessment Solved By Cell-Free DNA?

Share Tweet Share Share Email According to the recent milestone development of the National Institute of Health in California, a new blood test has been identified. The purpose of the test is to assess the gravity of the disease in patients with pulmonary…

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Ncbi Wgs Portal

Login page for ncbi wgs portal is presented below. Log into ncbi wgs portal page with one-click or find related helpful links. Last Updated: 17th August, 2022 WGS – NCBI – NIH   www.ncbi.nlm.nih.gov/genbank/wgs Nov 13, 2017 – Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or…

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CLINICAL CHARACTERISTICS AND PROGNOSTIC FACTORS IN PRIMARY BREAST DIFFUSE LARGE B-CELL LYMPHOMA

Keywords Diffuse large B-cell lymphoma, Breast, Prognostic factors, Relapse, Central nervous system References [1] C. Wiseman, and K.T. Liao, Primary lymphoma of the breast. Cancer 29 (1972) 1705-12.www.ncbi.nlm.nih.gov/pubmed/4555557 [2] P.J. Hosein, J.C. Maragulia, M.P. Salzberg, O.W. Press, T.M. Habermann, J.M. Vose, M. Bast, R.H. Advani, R. Tibshirani, A.M. Evens, N….

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New annotations in RefSeq – NCBI Insights

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms: Anopheles coluzzii (mosquito) Anopheles funestus (African malaria mosquito) Astyanax mexicanus (Mexican tetra) Athalia rosae (coleseed sawfly) Bactrocera dorsalis (oriental fruit fly) Brassica napus (rape) Brienomyrus brachyistius (bony fish) Canis lupus dingo (dingo) (pictured) Caretta…

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What is the function of this gene product in methylation?

This gene product helps to shift the emphasis of the methylation cycle toward the building blocks needed for new DNA synthesis, and away from the processing of homocysteine to methionine. [7] Also to know is, What is the role of non-CpG methylation? Because of its recent discovery, the role of…

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iPSCs – Pharmacology Group Discussion

iPSCs – Pharmacology Group Discussion – HackMD       Published Linked with GitHub # iPSCs – Pharmacology Group Discussion ## Neurology ### Reviews * [パーキンソン病に対する多能性幹細胞を用いた細胞移植治療の現状](https://doi.org/10.5692/clinicalneurol.cn-001235) * pdf * www.jstage.jst.go.jp/article/clinicalneurol/59/3/59_cn-001235/_article/-char/ja/ * doi * doi.org/10.5692/clinicalneurol.cn-001235 ### Trials * [Safety of the tau-directed monoclonal antibody BIIB092 in progressive supranuclear palsy: a randomised,…

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Job Application for C++ Software Developer in Bioinformatics and Big Data at NIH-NCBI

Overview Black Canyon Consulting (BCC) in partnership with Medical Science and Computing (MSC) is searching for a C++ Software Developer in Bioinformatics and Big Data to support the National Center for Biotechnology Information (NCBI).  This opportunity is full time and onsite at the NCBI in Bethesda, MD and/or remote work. NCBI,…

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Bronchoalveolar Lavage Fluid for Metagenomic Sequencing

Introduction Severe pneumonia is one of the most common causes of infectious diseases among patients in the intensive care unit (ICU), and this can lead to various complications and high mortality.1–3 Timely and accurate pathogen diagnoses are crucial for appropriate antimicrobial therapy and improved clinical outcomes. However, the low detection…

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Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…

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KEGG T01015: 107278078

Entry 4330855           CDS       T01015                                  Name (RefSeq) auxin-responsive protein SAUR32   KO K14488   SAUR family protein Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075   Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing  09132 Signal transduction   04075 Plant hormone signal transduction    4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Auxin_inducible Motif Other DBs…

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

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…

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Bioconductor – BSgenome.Gmax.NCBI.Gmv40

DOI: 10.18129/B9.bioc.BSgenome.Gmax.NCBI.Gmv40     Full genome sequences for Glycine max (Gmv40) Bioconductor version: Release (3.15) Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects. Author: Deisiany Ferreira Neres <deisianyufg at gmail.com> Maintainer: Deisiany Ferreira Neres <deisianyufg at gmail.com>, Clay…

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EnWik > Expasy

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution…

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How to identify DNA sequences with ambiguous nucleotides such as N, Y, R, W.. in a multifasta file and then remove these sequences with Biopython

How to identify DNA sequences with ambiguous nucleotides such as N, Y, R, W.. in a multifasta file and then remove these sequences with Biopython 4 Dear Biostars, My request is based on filtering and curing several multifastas. For instance, I have downloaded about 150 complete genomes from NCBI belonging…

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Development of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis

Cui, B., Smooker, P. M., Rouch, D. A., Daley, A. J. & Deighton, M. A. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling. J. Clin. Microbiol. 51, 9–14 (2013). CAS  PubMed  PubMed Central  Article  Google Scholar  Tevell, S., Hellmark, B.,…

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How to get the total number of unique genes affected by Pathogenic SNPs in dbSNP?

How to get the total number of unique genes affected by Pathogenic SNPs in dbSNP? 0 In dbVar I have been able to get the total number of unique genes affected by deletions, insertions and duplication which report classified this CNV as pathogenic. Now, I would like to do the…

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Researchers assess the evolution and diversity of monkeypox virus genomes using phylogenomic analysis

In a recent study published in Travel Medicine and Infectious Disease, researchers phylogenomically analyzed the monkeypox virus (MPXV). Study: Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage? Image Credit: ART-ur/Shutterstock Background Since May 2022, there have been various reports of increasing MPVX infections…

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Scientist I, Bioinformatics job at Vir Biotechnology in United States – 53516780

Vir Biotechnology is a commercial-stage immunology company focused on combining immunologic insights with cutting-edge technologies to treat and prevent serious infectious diseases. Vir has assembled four technology platforms that are designed to stimulate and enhance the immune system by exploiting critical observations of natural immune processes. Its current development pipeline…

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Root70 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/29/2015 14:17:23 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes::4,587 CDS::4,486 Pseudo Genes::46 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S, 23S) partial rRNAs:: tRNAs::51 ncRNA::1 ##Genome-Annotation-Data-END##…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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Screen.seqs result varying – Commands in mothur

I have a data set of 2×150 reads of 54 pairs of 16S v4 metagenomic sequences from NCBI sra of gastritis patients. When I previously ran the sequences through mothur, the screen.seqs after silva alignment removed sufficient number of sequences. mothur > screen.seqs(fasta=current, count=current, start=2, end=13426)Using Ulcer_Donors\stability.trim.contigs.count_table as input file…

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Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

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How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

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Gene Set – TNFSF10

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

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parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…

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Summary of Escherichia coli K-12 substr. MG1655, version 26.0

Summary of Escherichia coli, Strain K-12 substr. MG1655, version 26.0 Tier 1 Highly Curated Database Authors: Peter D. Karp1, Ingrid Keseler1, Carol Fulcher1, Anamika Kothari1, Suzanne Paley1, Markus Krummenacker1, Ian Paulsen2, Amanda Mackie2, Julio Collado-Vides3, Cesar Bonavides-Martinez3, Socorro Gama-Castro3, Alberto Santos-Zavaleta3, Victor H Tierrafria3 1SRI International, 2Macquarie University, 3Centro de…

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Index of /~ckern/FAANG_Project/Cattle_NCBI

Name Last modified Size Description Parent Directory   –   Aligned_Reads/ 2016-07-30 04:38 –   Cufflinks_Output/ 2017-11-11 11:53 –   FEELnc/ 2018-08-14 16:03 –   Gene_Expression/ 2016-09-01 14:14 –   Genome/ 2018-04-04 15:54 –   Intermediate_LncRNA.feelncclassifier.log 2016-08-05 15:59 18K   LncRNA/ 2018-08-08 11:07 –   Raw_Reads/ 2016-07-28 15:11 –  …

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How to identify locus_tag by using RefSeq protein info (WP_*)

How to identify locus_tag by using RefSeq protein info (WP_*) 0 Hi, I would like to know the locus tag of a protein annotated with RefSeq (WP_*). For example, I would like to identify the genomic location of a protein (WP_073031595.1) and also know its adjacent proteins. The GenBank file…

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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

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VCV000038126.28 Observations – ClinVar – NCBI

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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Metagenomics – RPKM calculation

Normalization for comparing gene coverage values. RPKM corrects differences in both: sample sequencing depth and gene length. RPKM – Reads per kilo base per million mapped reads Formula RPKM = numReads / ( geneLength/1000 * totalNumReads/1,000,000 ) numReads – number of reads mapped to a gene sequence geneLength – length…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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a strange pattern of repetitive summits

Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…

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Standard for aligning smallRNA to a reference human rRNA?

Standard for aligning smallRNA to a reference human rRNA? 0 Hi, I need to label some smallRNA sequences that I know are rRNA fragments. I know that for mRNA these are discarded by aligning to the human genome and filtering out multimapped reads, but I need to try to pin…

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Osteosarcoma Combination of Electroporation of Metabolic Modulators with Low dose chemotherapy

Osteosarcoma – Combination of Electroporation of Metabolic Modulators with Low dose chemotherapy Dr Kesh Gill Bone cancer particularly osteosarcoma can be an aggressive disease. Despite tremendous advances in diagnostic modalities, surgical procedures, and chemotherapy options, osteosarcoma confers a generally poor prognosis. The absence of an effective immune response to most…

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BAM file and no RNAME or POS information? : bioinformatics

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/incr_time.cpp Source File

Go to the documentation of this file. Go to the SVN repository for this file. 44  const string& driver_name, 47  m_InitTime = x_GetDoubleParam(conf, driver_name, params.m_Initial); 48  m_MaxTime = x_GetDoubleParam(conf, driver_name, params.m_Maximal); 49  m_Multiplier = x_GetDoubleParam(conf, driver_name, params.m_Multiplier); 50  m_Increment = x_GetDoubleParam(conf, driver_name, params.m_Increment); 55  const string& driver_name, 68  if (…

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difficulty filtering vcf file with vcftools

difficulty filtering vcf file with vcftools 1 I had a large VCF file named “common_known_variants.vcf ” which contains all known human variants downloaded from ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz -O common_known_variants.vcf.gz I’m trying to extract the known variants from only chromosomes 1,2,3,9,22, and X and write them in a new vcf file with the…

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Latest dbSNP VCF

This is the directory you’re looking for: ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/ curl -s ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.39.gz | zcat | head ##fileformat=VCFv4.2 ##fileDate=20210513 ##source=dbSNP ##dbSNP_BUILD_ID=155 ##reference=GRCh38.p13 ##phasing=partial ##INFO=<ID=RS,Number=1,Type=Integer,Description=”dbSNP ID (i.e. rs number)”> ##INFO=<ID=GENEINFO,Number=1,Type=String,Description=”Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a…

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SARS-COV-2 Blast : bioinformatics

Hello everyone I have multiple short sequences of SARS-COV-2 in the range of 500-800 nucleotides, I need to blast them, I get a good result on BLAST-NCBI, but is there anyone here who uses AudacityInstant which belongs to GISAID, this site aligns only sequences higher than 10000 nucleotides, as you…

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FastQ_7 April 2022(1) – Copy.pptx – What is the FASTA format? The FASTA format is the “workhorse” of bioinformatics. It is used to represent sequence

the FASTA format is not “officially” defined – even though it carries the majority of data information onliving systems. Its origins go back to asoftware tool calledFastawritten byDavidLipman(ascientist that later became, and still is, the director of NCBI) andWilliam R. Pearsonof the University ofVirginia. The tool itself has (to some…

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Mining Curated Databases for Literature in VSClinical

Curated databases are a real-time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Annotated file with gene ID (instead of gene symbol)

Annotated file with gene ID (instead of gene symbol) 0 @9cb59de3 Last seen 14 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am using a gtf file in the homepage of…

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PDT001259745.1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Date::03/08/2022 21:07:51 Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Provider::NCBI Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Annotation Software revision::2021-01-11.build5132 Genes (total)::5,850 CDSs (total)::5,754 Genes (coding)::5,653 CDSs (with protein)::5,653 Genes (RNA)::96 rRNAs::4, 2, 3 (5S, 16S, 23S) complete rRNAs::4 (5S) partial…

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GEO Browser – GEO – NCBI

Filter Mus musculus TSV Brian P. Hermann GSE109033 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells Expression profiling by high throughput sequencing Mus musculus 8 MTX TSV SRA Run Selector Brian P. Hermann Nov 06, 2018 GSE109037 10x Genomics Drop-seq single-cell…

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NCBI/mweb11 – WWW Error 404 Diagnostic

NCBI/mweb11 – WWW Error 404 Diagnostic The page you requested ( h t t p : / / w w w . n c b i . n l m . n i h . g o v / g e o / q u e r y / a…

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Cellosaurus cell line LCL-PI 202 (CVCL_B0QL)

Cell line name LCL-PI 202 Accession CVCL_B0QL Resource Identification Initiative To cite this cell line use: LCL-PI 202 (RRID:CVCL_B0QL) Comments Population: Iranian.Transformant: NCBI_TaxID; 10376; Epstein-Barr virus (EBV).Derived from sampling site: Peripheral blood. Disease Common variable immunodeficiency (NCIt: C26725)Common variable immunodeficiency (ORDO: Orphanet_1572) Species of origin Homo sapiens (Human) (NCBI Taxonomy:…

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Summary of Fusobacterium nucleatum MJR7757B, version 26.0

Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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ASM1860456v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/02/2021 10:26:31 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,541 CDSs (total)::3,440 Genes (coding)::3,416 CDSs (with protein)::3,416 Genes (RNA)::101 rRNAs::9, 9, 9 (5S, 16S, 23S) complete rRNAs::9, 9,…

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Why so much variability in RNA-seq technical replicates?

Why so much variability in RNA-seq technical replicates? 1 Hi all, I download an RNA seq data for gene expression analysis from NCBI. When I did counts with bedtools for my gene of interest, the variability was too much. Does that mean this data is unreliable? What could have caused…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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NCBI/mweb21 – WWW Error 404 Diagnostic

NCBI/mweb21 – WWW Error 404 Diagnostic The page you requested ( h t t p : / / w w w . n c b i . n l m . n i h . g o v / g e o / q u e r y / a…

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Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

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ASM1917534v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::08/30/2021 23:22:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,122 CDSs (total)::3,071 Genes (coding)::2,904 CDSs (with protein)::2,904 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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A hypoxia-related signature in lung squamous cell carcinoma

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

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SCO6471 – 100226_v2019_sA22-DBSCR15-RTB13 – Abasy Atlas

Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) [2019, A22-DBSCR15-RTB13, Weak + Strong] SCO6471 – Basal machinery kout: 0, kin: 1, Clustering: 0 Locus tag – SCO6471 UniProt ID – Q9ZBK3 NCBI GeneID – 1101910 GO terms GO:0016829 – Lyase activity GO:0046872 – Metal ion binding COGs COG2301…

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