Tag: ncbi

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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Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules

Li, Zhang, Yin, Yang, Du, Hou, Ge, Liu, Zhang, Zhang, Wu, Li, Liu, Wu, Song, Zhao, Shi, Deng (2011) Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules Cell Res 21(1) 196-204 Full text Abstract The introduction of four transcription factors Oct4,…

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NCBI RefSeq representative and reference genomes precalculated in PhenDB

News PhenDB now contains in the “Browse” section the trait precalculations for the reference genomes and representative genomes in NCBI RefSeq. The trait prediction results can be filtered by user-specific criteria for minimal prediction confidence and minimal balanced accuracy. Three figures demonstrate the number of positive and negative predictions for…

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socket.gaierror while downloading genbank files w/ biopython

The NCBI Entrez fetch API distinguishes return types rettype=”gb” and rettype=”gbwithparts”, the first can be shorter by giving you CONTIG lines referencing other records, while the later would expand these to give you the full sequence (look for “GenBank (full)” in the website). You can sometimes get a glimpse of…

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biopython – How can i write only a specific elements of the sequences, that i downloaded using Entrez.efetch, to the file( id and sequence itself)

I’m still a begginer at this. I downloaded 20 sequences from NCBI and my task is to allign them with themselves, but I need to separate the data, that I got using Entrez.efetch, so I could use it for allignment and I couldnt write the only specific elements (id and…

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ASM1863403v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/03/2021 14:29:20 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)::4,407 CDSs (total)::4,307 Genes (coding)::4,183 CDSs (with protein)::4,183 Genes (RNA)::100 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7,…

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Creating local nt blast database : bioinformatics

Hi all, I’m trying to create a local nt blast database, my eventual goal is to create a subset based on a taxanomic group to be used on a cluster with limited storage space, its seems the only way to do this though is to start with the whole database…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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VCV001049045.1 – ClinVar – NCBI

The TBP p.Gln87_Gln95del variant was not identified in the literature nor was it identified in dbSNP, ClinVar, Cosmic or LOVD 3.0. The variant was also not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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VCV000866285.4 – ClinVar – NCBI

Likely pathogenic (Feb 04, 2019) criteria provided, single submitter Method: clinical testing Retinal dystrophy Affected status: yes Allele origin: germline Blueprint Genetics Accession: SCV001239720.1 Submitted: (Oct 15, 2019) Comment: My Retina Tracker patient Likely benign (Dec 30, 2019) criteria provided, single submitter Method: clinical testing not provided Affected status: unknown…

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A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS  Google Scholar  Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….

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ASM1814142v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/07/2021 12:52:22 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)::4,858 CDSs (total)::4,780 Genes (coding)::4,742 CDSs (with protein)::4,742 Genes (RNA)::78 rRNAs::6, 6, 5 (5S, 16S, 23S) complete rRNAs::6, 6,…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

Continue Reading Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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ASM1922276v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::07/15/2021 15:46:43 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)::8,257 CDSs (total)::8,191 Genes (coding)::8,106 CDSs (with protein)::8,106 Genes (RNA)::66 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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BLASTn using R

BLASTn using R 0 Hello, I have around 2000 DNA nucleotide sequences (60 bases long) stored in each row in an excel sheet. I want to run BLAST over each one of them individually and extract the “Description” of the first hit. Like for Example: Suppose on NCBI BLAST website…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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ASM2099102v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::11/28/2021 12:10:22 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,454 CDSs (total)::3,291 Genes (coding)::3,252 CDSs (with protein)::3,252 Genes (RNA)::163 rRNAs::14, 13, 13 (5S, 16S, 23S) complete rRNAs::14, 13,…

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Search SRA Gateway for Metagenomics Data Wiki

Abstract The Sequence Read Archive (SRA)(https://www.ncbi.nlm.nih.gov/sra) houses all publicly available biological DNA sequence data to enhance reproducibility, reduce redundancy, and to allow for new discoveries by comparing data. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms and is growing at the alarming rate of 10…

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“No such file or directory: ‘test.xml”

Biopython NcbiblastpCommandline not working: “No such file or directory: ‘test.xml” 0 from Bio.Blast.Applications import NcbiblastpCommandline blastp=r”C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe” blastp_cline = NcbiblastpCommandline(blastp, query=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta”, db=r’C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta’, outfmt=5, evalue=0.00001, out=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.XML”) blastp_cline from Bio.Blast import NCBIXML with open(“test.XML”) as result_handle: E_VALUE_THRESH=0.01 blast_records = NCBIXML.parse(result_handle) blast_record = NCBIXML.read(result_handle) for alignment in blast_record.alignments: for hsp in alignment.hsps: if hsp.expect…

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Bioconductor – BSgenome.Amellifera.NCBI.AmelHAv3.1

DOI: 10.18129/B9.bioc.BSgenome.Amellifera.NCBI.AmelHAv3.1     Full genome sequences for Apis mellifera (Amel_HAv3.1) Bioconductor version: Release (3.14) Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within…

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Design and implementation of a novel pharmacogenetic assay for the identification of the CYP2D6*10 genetic variant | BMC Research Notes

Methods The study was conducted at the Human Genetics Unit, Faculty of Medicine, University of Colombo. It was an experimental study, where a novel assay was designed for the targeted variant, and a cohort of hormone receptor positive breast cancer patients were genotyped for the CYP2D6*10 variant using the optimized…

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ASM1890591v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::12/19/2021 14:49:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,956 CDSs (total)::2,892 Genes (coding)::2,846 CDSs (with protein)::2,846 Genes (RNA)::64 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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From scientific name to taxonomy information entrez

From scientific name to taxonomy information entrez 1 Hi all, I have a txt file with a list of scientific names of plants and I would like to obtain a final file with taxonomy information. For example, if one of my organism is Acalypha hispida, I would like to obtain…

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Top 17 b cell lymphoma treatment in 2022

Below are the best information and knowledge on the subject b cell lymphoma treatment compiled and compiled by our own team tuhoangkaido: 1. Treating B-Cell Non-Hodgkin Lymphoma 2. Treatments for B-Cell Lymphoma 3. Diffuse Large B-Cell Lymphoma: Treatment Options 4. B-cell Lymphoma 5. B-cell Lymphoma: Types, Symptoms & Prognosis 6….

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OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)

The organism package org.Hs.eg.db is updated twice a year in March and September, a week or two before each Bioconductor release. The current version of Org.Hs.eg.db is dated 15 September 2021. org.Hs.eg.db is 100% comprehensive in that it contains all Entrez IDs that exist at the time it is created….

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VCV000698353.6 – ClinVar – NCBI

Likely benign (Nov 17, 2018) criteria provided, single submitter Method: clinical testing Arrhythmia Affected status: unknown Allele origin: germline Color Health, Inc Accession: SCV001358509.1 Submitted: (May 19, 2020) Likely benign (Apr 19, 2020) criteria provided, single submitter Method: clinical testing Long QT syndrome Affected status: unknown Allele origin: germline Invitae…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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Index of /~psgendb/doc/pkg/NCBI/errmsg

Name Last modified Size Description Parent Directory   –   a2ferr.msg 2011-05-17 19:57 3.8K   flat2asn.msg 2011-05-17 19:57 13K   htgs.msg 2011-05-17 19:57 739   indx_err.msg 2011-05-17 19:57 4.2K   medarch.msg 2011-05-17 19:57 356   pir2asn.msg 2011-05-17 19:57 2.2K   taxarch.msg 2011-05-17 19:57 142   taxutil.msg 2011-05-17 19:57 142  …

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METASnake: a Snakemake workflow to facilitate…

Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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NCBI BlastRule accession NBR015122

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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KEGG T01001: 5105

Entry 5106              CDS       T01001                                  Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial   KO K01596   phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa  Homo sapiens (human) Pathway hsa00010   Glycolysis / Gluconeogenesis hsa00020   Citrate cycle (TCA cycle) hsa00620   Pyruvate metabolism hsa01100   Metabolic pathways hsa03320   PPAR signaling pathway hsa04068   FoxO signaling pathway hsa04151   PI3K-Akt signaling…

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LAMP-CRISPR-Cas12a-lateral flow immunochromatographic strip | IDR

Introduction About 700,000 people die from “superbugs” globally every year. Antibiotic abuse is the culprit of extensive spread of superbugs. Currently, carbapenemase-producing organisms are among the most important pathogens of hospital infections. Especially the plasmid-mediated highly transmissible carbapenem-resistant Enterobacterales (CRE) has become an important public health issue of global concern….

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Bacterial 23S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 23S 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 National Center for…

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ASM1993088v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::09/24/2021 10:50:11 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,022 CDSs (total)::3,966 Genes (coding)::3,901 CDSs (with protein)::3,901 Genes (RNA)::56 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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GPP Web Portal – Transcript Details

Transcript: Human XR_933717.2 PREDICTED: Homo sapiens uncharacterized LOC105371334 (LOC105371334), ncRNA. Source: NCBI, updated 2019-09-08 Taxon: Homo sapiens (human) Gene: LOC105371334 (105371334) Length: 321 CDS: (non-coding) sgRNA constructs matching this transcript (CRISPRko, NGG PAM) This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the exonic sequence of…

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Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Rat Anti-Mouse CD25/IL-2R Antibody

Name Rat Anti-Mouse CD25/IL-2R Antibody (GWB-31929F) Related Product Names Rat Anti-Mouse CD25/IL-2Ra-PE; PMP-22; Protein CD25; SR13 myelin protein; Schwann cell membrane glycoprotein; SAG Cd25; Pmp-22Rat Anti-Mouse CD25/IL-2RPmp22 Gene Symbol IL2RA Gene Fullname Interleukin-2 receptor subunit alpha Gene id 3559 Swissprot ID P01589 Protein Name Interleukin-2 receptor subunit alpha Protein Accession…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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API for NCBI Accession ID (GenBank or RefSeq ) generation from a list of species names?

Hi Rijan, Just to be sure I understand what you want: you have a list of species and you would like to get the accession numbers for the reference genomes for each one of them, is that correct? If so, you could try using the command datasets summary in combination…

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API for NCBI Accession ID (GenBank or RefSeq) generation from a list of species names? : bioinformatics

TL;DR: How can I convert a list of species names (common or scientific) into a corresponding list of NCBI database accession IDs to download the respective species’ reference genome from NCBI. The NCBI urls’ are not common or scientific name compatible so a regular python script for web scrapping that…

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KEGG T03334: R50912_07385

Entry R50912_23945      CDS       T03334                                  Name (GenBank) alpha-galactosidase   KO K07407   alpha-galactosidase [EC:3.2.1.22] Organism paeq  Paenibacillus sp. FSL R5-0912 Pathway paeq00052   Galactose metabolism paeq00561   Glycerolipid metabolism paeq00600   Sphingolipid metabolism paeq01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:paeq00001] 09100 Metabolism  09101 Carbohydrate metabolism   00052 Galactose metabolism    R50912_23945  09103 Lipid metabolism   00561 Glycerolipid metabolism    R50912_23945   00600 Sphingolipid metabolism    R50912_23945Enzymes [BR:paeq01000] 3. Hydrolases  3.2  Glycosylases   3.2.1  Glycosidases, i.e. enzymes that hydrolyse O-…

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The Difference Between Genome Reference(scRNAseq) And Transcriptome Reference(bulk RNAseq)

I want to know the difference between Genome Reference in scRNAseq and transcriptome reference in bulk RNAseq. But I didn’t get any better answer in any other place. I know we could download genome reference from UCSC, NCBI, ENSEMBL and GENECODE for bulk RNAseq. And here are the links below:…

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UniProt: A0A1S3QEZ7_SALSA

ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…

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RefSeq: XP_007190711

LOCUS XP_007190711 296 aa linear MAM 12-FEB-2019 DEFINITION reticulon-4-interacting protein 1, mitochondrial isoform X3 [Balaenoptera acutorostrata scammoni]. ACCESSION XP_007190711 VERSION XP_007190711.1 DBLINK BioProject: PRJNA237330 DBSOURCE REFSEQ: accession XM_007190649.2 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata scammoni ORGANISM Balaenoptera acutorostrata scammoni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea;…

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Vertical stratification of the air microbiome in the lower troposphere

Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

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dbSNP – Wikipedia @ WordDisk

The Single Nucleotide Polymorphism Database[1] (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). Although the name of the database implies a collection of…

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