Tag: ncbi

How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

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taxonomy – Assign multiple taxids to a sequence when constructing a local BLAST database

I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two or more taxids separated by a semicolon, such as 556514;701533. Fixing the script to handle this should be fairly straightforward. But the…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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[BioC] problem with GEOquery

Hi to everybody, i have a little problem with GEOquery .i when I’m trying to download the GSE2841 dataset I encounter the gse <- getGEO(“GSE2841”) try with URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz’Error in downloading the.file(myurl, destfile, mode = mode) :impossible to open URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz'&#8221; why???????????? Please help me Best regards Dr Alberto GoldoniMedical Genetics UnitS….

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NCBI looking for testers for a new web-only (for now) clustered `nr` database

News:NCBI looking for testers for a new web-only (for now) clustered `nr` database 0 Find details about how to participate by going to this link. Clustered nr is the standard NCBI nr database clustered with each sequence within 90% identity and 90% length to other members of the cluster. Your…

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Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project We’re sorry, but GBIF doesn’t work properly without JavaScript enabled. Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. Citation McVeigh R (2013)….

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Convert list of Accession Numbers to Full Taxonomy

Using NCBI Entrez direct. $ esearch -db assembly -query “GCA_000005845” | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F “>|<” ‘BEGIN{ORS=”, “;}{print $3;}’ Escherichia coli str. K-12 substr. MG1655, cellular organisms, Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, If…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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Why is mtDNA maternal only? : explainlikeimfive

Mitochondria are kind of like an in-between of cell-organelles and bacteria that live in your cells. They are not made by your cells, but they replicate on their own (by splitting in two). For this, they use their own DNA (the mtDNA), not the DNA of your cells. When an…

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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an R package for interactive visualization of multi-omics data and annotation of chromosomes

Additional file 1. Example of chromoMap interactive plot constructed using various features of chromoMap including polyploidy (used as multi-track), feature-associated data visualization (scatter and bar plots), chromosome heatmaps, data filters (color-coded scatter and bars). Differential gene expression in a cohort of patients positive for COVID19 and healthy individuals (NCBI Gene…

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ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics

1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article  Google Scholar  2. Minio A, Lin J, Gaut BS, Cantu D. How single…

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Annotation of alternative cattle genome assembly

University of Maryland have assembled the cattle genome and in severalways we find this to be better than the Baylor assembly. Several groups including ours are using this version ofthe assembly. ftp.cbcb.umd.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.0/ NCBI has agreed to provide annotations for this version of the assemblyalso. I request you to host this…

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Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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NCBI BlastRule accession NBR000207

NCBI BlastRule accession Model protein Product name Family type Gene symbol EC number(s) GO term(s) Identity cutoff (%) Target coverage cutoff (%) Model coverage (%) Number of RefSeq protein hits counting … Named by this model (…) Other hits (…) No RefSeq protein is named by this evidence. Failed to…

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ASM1584570v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Date::05/22/2015 10:24:41Annotation Method::Best-placed reference protein set; GeneMarkS+Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Provider::NCBIFeatures Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionAnnotation Software revision::2.10 (rev. 463717)Genes::5,665CDS::5,280Pseudo Genes::271CRISPR Arrays::4rRNAs::32 (5S, 16S, 23S)tRNAs::82ncRNA::1Frameshifted Genes::68##Genome-Annotation-Data-END## Read more here: Source link

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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MARS seq alingment

MARS seq alingment 0 Hello everyone, new here and also new to the field. was asked to create a pipeline for RNA seq and after two months of self learning of how to interact with each code im stuck with the program STAR. what im trying to do for now…

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Associate Director, Bioinformatics Job Opening in Wilmington, DE at Incyte Corporation

Incyte is a biopharmaceutical company focused on the discovery, development, and commercialization of novel medicines to meet serious unmet medical needs in oncology and inflammation and autoimmunity. Incyte is committed to the rigorous pursuit of research and development excellence to improve the lives of patients, make a difference in health…

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Getting peak heights from TF chIP-seq data (wig file)

Getting peak heights from TF chIP-seq data (wig file) 1 Hello everyone, I have TF ChIP seq data from NCBI GEO in wig format. I converted wig to bedgraph and then used MACS peak caller to get bed narrowpeak files.I further uploaded file on genome browser to get graphical map…

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shRNA Adeno-associated Virus Serotype 2, p7SK-(OR8D1-shRNA-Seq5) (AAV-SI3323WQ)

For Research Use Only. Do NOT use in humans or animals. This product is a OR8D1-shRNA encoding AAV, which is based on AAV-2 serotype. The OR8D1 gene encodes a olfactory receptor protein that interacts with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of…

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Toll-like receptor 2/4 in Chinese patients with sepsis

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…

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SAMD9

cite web | title = Entrez Gene: SAMD9 sterile alpha motif domain containing 9| url = www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=54809| accessdate = ] PBB_Summarysection_title = summary_text = References Further reading PBB_Further_reading citations = *cite journal | author=Maruyama K, Sugano S |title=Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with…

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UMass Chan Medical School hiring Research Lab Tech I – Neurogenerative Disease (CRISPR-Cas gene editing) in Worcester, Massachusetts, United States

OverviewGENERAL SUMMARY OF POSITION: We are seeking a Research Technician to work collaboratively on CRISPR-Cas gene editing of the Huntington’s Disease (HD) gene. HD is a devasting neurodegenerative disease that currently has no effective treatment. Our goal is to develop gene editing methods to inactivate or correct the disease-causing version…

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KEGG T01005: 453503

Entry 453503            CDS       T01005                                  Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3   KO K17917   sorting nexin-1/2 Organism ptr  Pan troglodytes (chimpanzee) Pathway ptr04144   Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    453503 (SNX1) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:ptr04131]    453503 (SNX1)  09183 Protein families: signaling and cellular processes   04990…

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dbSNP specific to C57BL6J

dbSNP specific to C57BL6J 0 Hi is it possible to obtain a dbSNP file that is specific to a strain e.g. C57BL6J? I tried looking for it in the ncbi, MGI and Jackson website. But I don’t seem to find strain specific vcf. Thanks c57bl6j dbsnp • 39 views •…

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makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version of BLAST (Version 2.11.0+) and downloaded the refseq_protein database from NCBI using the following code wget ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz The database gets downloaded…

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VCV000445854.7 Observations – ClinVar – NCBI

1 SCV000610624.1 Center for Pediatric Genomic Medicine,Children’s Mercy Hospital and Clinics Benign criteria provided,single submitter clinical testing not provided (not provided ) germline 1 SCV000700353.2 Eurofins NTD, LLC Uncertain significance criteria provided,single submitter clinical testing 1 not provided (unknown ) germline 1 Single Heterozygote www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP21A2 mixed 1 SCV001137083.1 Mendelics Benign…

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hg38 Import custom reference upload error

Our version of TS is 5.12.2 When trying to upload new custom reference fasta (downloaded from ncbi ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz, gunzipped and renamed to hg38.fasta) through “Import custom reference” in interface an error occures: “uploaded file size is incorrect” (to be honest the error was not shown in logs, because of TypeError…

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sequence alignment – Help with MinION sequencing data species identification

Hi I’m new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi…

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Long read de novo phylogenetic tree for metagenome

Long read de novo phylogenetic tree for metagenome 0 What tools are available to create de novo phylogenetic trees for long read metagenome datasets? phyloT seems to construct one based on taxonomy and NCBI/GTDb information rather than read alignment. Is MAFFT commonly used? What is the standard methodology? (For reference,…

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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis

1. Eyun, S. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol. Biol. 17, 23 (2017). PubMed  PubMed Central  Google Scholar  2. Eyun, S. et al. Evolutionary history of chemosensory-related gene families across the Arthropoda. Mol. Biol. Evol. 34, 1838–1862 (2017). CAS  PubMed …

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Clinical Bioinformatics Analyst (m/w/d) – Foundation Medicine GmbH – Biology & Life Sciences

Clinical Bioinformatics Analyst (m/w/d) PENZBERG, GERMANY Foundation Medicine is leading a transformation in cancer care, where each patient’s treatment is informed by a deep understanding of the molecular changes that contribute to their disease. As a molecular information company, we are focused on fundamentally changing the way in which patients…

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Bioconductor – BSgenome.Hsapiens.NCBI.GRCh38

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.NCBI.GRCh38     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.NCBI.GRCh38. Full genome sequences for Homo sapiens (GRCh38) Bioconductor version: 3.11 Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. Author: The…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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some signatures that have been suppressed by RefSeq/GenBank are not in wort

For example, the following accessions have been “suppressed” in RefSeq and GenBank, and do no appear in wort (/group/ctbrowngrp/irber/data/wort-data/wort-genomes/sigs/<accession>.sig). I checked newer version numbers and still did not find these accessions (e.g. GCA_900474135*sig). Looking on GenBank, I see the record has been suppressed/removed: www.ncbi.nlm.nih.gov/assembly/GCF_900474135.2/ GCA_900474135.2 GCA_002798115.1 GCA_001308105.1 I couldn’t find…

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bioinformatics – Local BLAST NCBI C++ Exception

I’m getting an error trying to to use blast v2.12 against a local nt database. I’ve downloaded nt twice from the ftp server thinking the first time it was corrupt but that didn’t change anything. My command is: blastn -db nt -num_threads 8 -outfmt “6 qseqid sacc stitle ssciname nident…

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How to differenciate between 16s hypervariables regions using QIIME2 ? – User Support

M_F: May i search the sequences on ncbi for example correponding to v4 domain No, NCBI probably would not have such sequences in an easily indexed form but I could be wrong. Rather, grab some reference sequences (can be a random subsample, do not need all of them) and use…

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RefSeq-announce Info Page

RefSeq-announce — Public RefSeq Release announcements   About RefSeq-announce This mail list is used to announce changes or updates to the NCBI RefSeq collection. Announcements will be made for full RefSeq Releases to the FTP site. Additional mail may be sent when large genomes are added to the collection, or…

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VCV001048762.1 – ClinVar – NCBI

Pathogenic (-) no assertion criteria provided Method: clinical testing Secondary hypothyroidism (Autosomal recessive inheritance) Allele origin: germline Department of Clinical Genetics and Genetic Counseling,Mediscan Systems Accession: SCV001548494.1 Submitted: (Apr 05, 2021) Evidence details Publications PubMed (1) Comment: The p.Ala37LeufsX38 mutation is not reported in the literature so far, however it…

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16S rRNA gene amplicon sequence data from sunflower endosphere bacterial community

doi.org/10.1016/j.dib.2021.107636Get rights and content Abstract Insights into plant endosphere bacterial diversity and exploration of their bioincentives in the formulation of biofertilizers promise to avert ecological disturbances. Here, we presented the sequence dataset of the endophytic bacterial community from the roots and stems of sunflower obtained from farmlands in Itsoseng and…

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Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine – University of Calgary – job portal

University of Calgary Home Prospective Students Current Students Alumni Community Faculty & Staff Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Share this Job: Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine Job ID: 24643 Updated:…

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computeMatrix in deeptool is Running with no result

computeMatrix in deeptool is Running with no result 0 Hi All, I wonder if someone can help me in explaining what to input on the -R <bed file> argument of the code below? computeMatrix scale-regions -S <bigwig file(s)> -R <bed file> -b 1000 what I did for example, I download…

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[Analysis of the Differential Expression of circRNA in Acute Myeloid Leukemia by GEO Database]

Objective: To investigate the difference expression of circular RNA (circRNA) in acute myeloid leukemia (AML) by using bioinformatics method. Methods: The microarray chip data of AML was searched and downloaded from the Gene Expression Omnibus (GEO) of the National Center for Bioinformatics (NCBI). The differences between AML samples and control…

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Sr Scientist – IVD Development – Houston

NuProbe USA Inc . is looking for a Staff/Senior Scientist to lead the IVD project development program at NuProbe to support both research and in vitro diagnostic (IVD) assays for use in medical research, clinical trials, regulatory submissions, and clinical diagnostic use.  NuProbe USA is a rapidly growing company and…

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Summer Intern -Bioinformatics – Roche – Pleasanton

·  Job facts Summer Intern – (Bioinformatics) The Summer @ Roche Intern Program has been developed to provide students with a fun yet rewarding summer through hands-on experience and numerous opportunities to network with other interns as well as employees in the organization. Additionally, we help our students meet their…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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18S gene not present in genome assembly?

18S gene not present in genome assembly? 0 I am designing PCR primers to amplify a region of the 18S rRNA gene of Penicillium expansum. As the template for primer design, I use the consensus sequence of a multiple sequence alignment of 18S sequences obtained from the SILVA database. When…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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Kraken2

Kraken2 0 I wanted to make a kraken database but i got this error while running the command.I am using Kraken2 $ kraken2-build –standard –threads 24 –db kraken2database/ Downloading nucleotide gb accession to taxon map… done.Downloading nucleotide wgs accession to taxon map… done.Downloaded accession to taxon map(s)Downloading taxonomy tree data……

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Bioinformatics Librarian job with University of Pennsylvania

Bioinformatics Librarian University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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Load .gb file in R

Hello community, I am trying to load the .gb file I got after blast on ncbi. Tried a few libraries, like “genbankr”, “read.gb”, but without success. I got the following error: library(read.gb) read.gb(“orig_with_blast.gb”, DNA = TRUE, Type = “full”, Source = “File”) Error in eval(parse(text = Order[i])) : object ‘ORGANISM’…

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What is the single nucleotide polymorphism database ( dbsnp )?

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…

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ASM648341v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/22/2018 18:06:09 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,178 CDS (total)::7,112 Genes (coding)::6,886 CDS (coding)::6,886 Genes (RNA)::66 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM296653v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/19/2021 18:16:01 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,877 CDSs (total)::1,821 Genes (coding)::1,767 CDSs (with protein)::1,767 Genes (RNA)::56 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2,…

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Getting sequence from any fasta based on coordinates

Getting sequence from any fasta based on coordinates 1 I have received coordinates of several genes (not annotated) and was said the origin is TAIR10. I wanted to extract these sequences based only on this information, but encounter several doubts. I know it seems trivial but I am curious whether…

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Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Genome organization and structure of O. laetus The MiSeq data of BTI and CBE samples of O. laetus was submitted to the NCBI SRA database under the accession numbers SRR11024516 and SRR11024517, respectively. The study was done to understand whether there exists a different species of the genus Oxycarenus similar…

Continue Reading Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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NCBI datasets bulk protein fasta download

NCBI datasets bulk protein fasta download 0 Hi, I want to download protein fasta files for a set of bird species. I have the genome assembly accessions in a file. I feel like every time I need to bulk download fasta files I’ve forgotten how I did it last time…

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Adding new taxa to a Kraken2 db

Hi, can someone please check if these following steps are correct? I am trying to add to my plants kraken2 db (“plant_original”) few taxa genomes that I have downloaded from the NCBI website (alnus_glutinosa_GCA_003254965.1.fna, carpinus_fangiana_GCA_006937295.1.fna etc..). for file in *.fna do kraken2-build –add-to-library $file –db PATH/kraken/plant_original done Masking low-complexity regions…

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ASM350094v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/27/2018 21:42:42 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,542 CDS (total)::3,498 Genes (coding)::3,451 CDS (coding)::3,451 Genes (RNA)::44 tRNAs::40 ncRNAs::4 Pseudo Genes (total)::47 Pseudo Genes (ambiguous residues)::2 of 47 Pseudo…

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How to extract genomic upstream region of a protein identified by its NCBI accession number?

How to extract genomic upstream region of a protein identified by its NCBI accession number? 1 I have a list of NCBI protein accession numbers. I would like to extract out the upstream genomic region of the corresponding gene’s nucleotide sequence. I will be thankful to you if you can…

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BLAST multiple sequences against each other from one FASTA file

BLAST multiple sequences against each other from one FASTA file 1 Hi, I am a beginner to using BLAST locally on Mac OSX. I have downloaded ncbi-blast-2.2.31+.dmg and have installed it. I have a FASTA file with multiple protein sequences in it and am trying to BLAST each sequence against…

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What does it mean BLASTx in de novo RNAseq analysis?

What does it mean BLASTx in de novo RNAseq analysis? 1 Hi, all. I try to get an assembly stat. According to some articles, it tends to have information that can be obtained by BLAST. For example, “Top BLASTx-hit species” and “Percent of gene with at least one BLASTx hit…

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Biopython Contact Us | Contact Information Finder

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

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Transcriptome assembly, annotation and submission to GenBank for unannotated organisms

Monday, October 4 at 3:00pm to 4:00pm Virtual Event Transcriptome assembly and annotation is a complex process that requires the integration of multiple databases using several computational tools for best results. The advances in next-generation sequencing technologies and the decrease in the cost of sequencing a complete transcriptome are driving…

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Co-op DNA Sequencing QC/QA – Addgene

Company Description Addgene is a thriving nonprofit founded in 2004 that facilitates biomedical research and discovery. Our biorepository stores, archives, and distributes plasmids for scientists around the world. Addgene’s plasmid collection is used to advance research in a wide variety of disciplines, including cancer, heart disease, and neurodegenerative disorders, and…

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Improving processing and quality of DNA data for biodiversity research

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…

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ASM314399v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/15/2018 16:18:51 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,893 CDS (total)::1,839 Genes (coding)::1,782 CDS (coding)::1,782 Genes (RNA)::54 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::3, 1 (5S, 16S) partial…

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How To Download .Gbk Files From Ncbi Website

How To Download .Gbk Files From Ncbi Website 1 how to download .gbk files from ncbi website? ncbi download genbank • 25k views • link updated 38 minutes ago by Ram 34k • written 9.8 years ago by Arun • 0 Search for the sequence that you want. The “display…

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Exporting normalized counts data from DeSeq2

Exporting normalized counts data from DeSeq2 1 Hi, I am working with large RNA-Seq dataset downloaded from the NCBI GEO. I would like to export the normalized counts data from DeSeq2 based on size factor normalization for further downstream analysis. It seems like running dds <- DESeq(dds) and dds <-…

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Submit sequence data to NCBI

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…

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Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

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How to download all the genome fasta file for plants?

How to download all the genome fasta file for plants? 1 Hello, I want to download all genome fasta file of plants from NCBI for executing stand alone blast. Please share any command line tools are available. Thank you Mathavan M standalone blast • 68 views NCBI Datasets is specifically…

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Precomputed secondary structure prediction from sequence

Precomputed secondary structure prediction from sequence 2 Hi, Most services that predict secondary structure from sequence, such as psipred, have an online webserver or a program you’d have to run locally (which would take quite a bit for a whole proteome). e.g. bioinf.cs.ucl.ac.uk/psipred/result/0fc9a438-c3d8-11e3-a745-00163e110593 I was wondering if anyone knew a…

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Combining RNA-Seq read counts from 2 lanes of the same sample (.txt file)

Hi, I have a question on combining read counts from 2 lanes of the same sample. I have a very large RNA-Seq dataset downloaded from the NCBI GEO. The data files are in the *.txt format and each sample with 2 lanes obtained from featureCounts. I would like to perform…

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ASM1227490v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/09/2021 05:00:21 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,608 CDSs (total)::4,469 Genes (coding)::4,408 CDSs (with protein)::4,408 Genes (RNA)::139 rRNAs::10, 9, 9 (5S, 16S, 23S) complete rRNAs::10, 9,…

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GenBank Biologist – Bethesda, MD

Job Description Interested in an exciting and rewarding alternative career in the biosciences? Tired of bench work? Enjoy puzzles and problem solving? Incredibly detail oriented? If you answered yes to these questions, consider joining our team of highly skilled and dedicated scientists working on site at the National Center for…

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deepmind alphafold github

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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Standard Bioinformatics Analysis of RNAseq data (DGE, Pathway Enrichment, Network analysis) – Freelance Job in Quantitative Analysis – Less than 30 hrs/week – Less than 1 month

We are looking for bioinformatics help to analyze specific data sets available from GEO / NCBI using standard bioinformatics analysis pipeline We will provide the study, design and data We will ask you to create a standard bioanalytical report that will include :– Differential gene expression, clustering – Pathway enrichment/analysis–…

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ASM298219v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::01/12/2021 08:24:12 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,192 CDSs (total)::5,077 Genes (coding)::4,870 CDSs (with protein)::4,870 Genes (RNA)::115 rRNAs::9, 8, 8 (5S, 16S, 23S) complete rRNAs::9, 8,…

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Bioinformatician I/II/III – Job posted on PostdocJobs.com

Job Description Farmington, Connecticut Apply Summary The Robinson lab is seeking a Bioinformaticician to join our team that focuses on the development of software and ontologies for biomedical research. Our team of expert biological curators, bioinformaticians, and computer scientists maintain and enhance a knowledge extraction and refinement process that delivers…

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Why some SNP’s are not assigned to any gene?

Why some SNP’s are not assigned to any gene? 0 Hi everyone, I am doing polygenic risk analysis (PRS) ; As you may know PRS is done based on SNP’s. On the other hand, I would like to do some visualizations at gene level. Thus, I used rsnps library (ncbi_snp_query…

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NCBI nucleotide ID to protein ID

NCBI nucleotide ID to protein ID 1 Dear all, I have some NCBI nucleotide ID, about 4,000. I want to download it’s protein sequence from NCBI. I know we can download the fasta format using “NCBI batch”, but the problem is that I can not download the protein sequence using…

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BLASTP version 4 database error *Help

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

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Whole genome sequencing and RNA sequencing data analysis for a bacterial strain

Whole genome sequencing and RNA sequencing data analysis for a bacterial strain 1 Hello, I am new RNA sequencing work. I have raw fastq files (from extracted RNA and DNA both) for bacteria “Paucibacter toxinivorans strain IM4”. I am not able to find whole reference genome for the same bacteria….

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How can I get PHRED score?

How can I get PHRED score? 1 Hi, all. I am trying to get the assembly stat(Table S1.) according to the following paper about de novo assembly. [www.ncbi.nlm.nih.gov/pmc/articles/PMC7266049/%5D%5B1] In the table, there is an item “Mean read PHRED score after filtering and trimming”. How can I get this? Is there…

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Answer: Error during prefetch

Maybe a connection problem, not unusual with NCBI. There is no need to bother with the NCBI Toolkits, you can get fastq files directly with links from e.g. sra-explorer.info If you visit that website (which is a wrapper around the NCBI and ENI APIs) and enter your accession it will…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Use one few genes instead of reference genome in mapping

Use one few genes instead of reference genome in mapping 0 Hi. My aim is to generate a phylogenetic tree from my analysis. For this, I have a reference genome and Illumina reads of multiple samples. I was thinking of using my own gene list generated from sequences downloaded from…

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How to map SILVA taxa names to NCBI IDs (in R)?

How to map SILVA taxa names to NCBI IDs (in R)? 0 Hi, How to map taxonomy assigned using SILVA database to NCBI ID (preferably in R)? I’m using R Dada2 and SILVA database to assign taxonomy: Bacteria > Firmicutes > Bacilli > Lactobacillales > Enterococcaceae > Enterococcus I need…

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