Tag: CDS

Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures

Summary Background Inter-individual variability during sepsis limits appropriate triage of patients. Identifying, at first clinical presentation, gene expression signatures that predict subsequent severity will allow clinicians to identify the most at-risk groups of patients and enable appropriate antibiotic use. Methods Blood RNA-Seq and clinical data were collected from 348 patients…

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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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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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Monocle3 differential expression failed when active.assay is not “RNA”

after run estimate_size_factors, data with active.assay = ‘integrated’ works too, but no deg in the result. > [email protected] = ‘integrated’ > cds_raw <- as.cell_data_set(seurat_object) Warning: Monocle 3 trajectories require cluster partitions, which Seurat does not calculate. Please run ‘cluster_cells’ on your cell_data_set object > cds <- cluster_cells(cds_raw) > pr_graph_test_res <-…

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Bioinformatician – qPCR and annotation directions Jobs at Nalagenetics, Jakarta

We are hiring a bioinformatics specialist interested in developing a clinical decision support for implementation of genetics in clinical settings. The person will be responsible of building analytical pipelines forpatients’ genomic, demographic, and individual data, as well as working with our senior software engineer tointegrate our knowledge base with existing…

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AAV ShRNA Cloning Service – CD Biospeeds

AAV ShRNA Cloning Service AAV ShRNA Cloning Service Adeno-associated virus (AAV) is a type of parvovirus. Its genome is single-stranded DNA and has the ability to infect both dividing and non-dividing cells. Adenovirus or herpes virus is usually needed to help it replicate and expand in the…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

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PyTorch running on top of ROCm on a 6800M (6700XT) laptop! Took a ton of minor config tweaks and a few patches but it actually functionally works. HUGE! : Amd

This is actually a case where Windows is behind. You want to do DNNs, you go to Linux (and NVIDIA). Edit: By the way, that is not to say that Linux isn’t still a shitty experience. We have a DGX Station A100 at work, and the NVIDIA people came around…

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htseq-count Error ‘_StepVector_Iterator_obj’ object has no attribute ‘next’

htseq-count Error ‘_StepVector_Iterator_obj’ object has no attribute ‘next’ 0 I am trying to run htseq-count (v. 0.13.5) on a sorted and indexed bam file. The command I entered looks like this: htseq-count -f bam -r pos -s yes -t CDS -i gene_id -m union filename_sorted.bam filename.gtf I get the following…

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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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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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SnpEff does not create htmlStats

SnpEff does not create htmlStats 0 SnpEff does not create htmlStats with the below command: $ snpEff eff -Xmx20G LAB330 LabUsa16cWild01-20_L-Q.vcf | head ##fileformat=VCFv4.0 ##filedate=20210414 ##source=SGSautoSNP ##reference=NbLab330.genome.softmasked.fasta ##phasing=allhomozygote ##INFO=<ID=DP,Number=1,Type=Integer,Description=”Read depth over all samples”> ##INFO=<ID=PL,Number=0,Type=String,Description=”Panel”> ##SnpEffVersion=”5.0e (build 2021-03-09 06:01), by Pablo Cingolani” ##SnpEffCmd=”SnpEff LAB330 LabUsa16cWild01-20_L-Q.vcf ” ##INFO=<ID=ANN,Number=.,Type=String,Description=”Functional annotations: ‘Allele | Annotation…

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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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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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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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Percent identity matrix from ClustalOmega/Clustalw with Biopython

I have a set of sequences for the YPR193C coding sequence from various yeast strains. I would like to get the percent identity matrix from multiple sequence alignments using ClustalW, Clustal Omega, or MUSCLE using the Biopython wrappers. This should be possible for ClustalW and Clustal Omega based on the…

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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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Extract root(start) and leaf(end) states programmatically in monocle2

Extract root(start) and leaf(end) states programmatically in monocle2 0 Dear bioinformaticians, do you know how to extract starting state and end states from the CDS in monocle2 ? I know I can detect them visually inspecting the States plot after I compute the pseudotime. I am asking if there is…

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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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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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Cosmo_00080 : CDS information — DoBISCUIT

Category 1.1 PKS Product polyketide synthase chain length factor subunit Product (GenBank) CosC Gene Gene (GenBank) cosC EC number Keyword Note Note (GenBank) ketosynthase – beta subunit Reference ACC Q2PZR8 PmId [16810496] Insights in the glycosylation steps during biosynthesis of the antitumor anthracycline cosmomycin: characterization of two glycosyltransferase genes. (Appl…

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ASM212806v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/12/2020 21:58:49 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.13 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::767 CDSs (total)::724 Genes (coding)::684 CDSs (with protein)::684 Genes (RNA)::43 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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Pact_00210 : CDS information — DoBISCUIT

Category 3.4 other modification Product putative 6-methylsalicylyltransferase Product (GenBank) ketoacyl-ACP synthase Gene pctTptmR Gene (GenBank) pctT EC number Keyword Note Note (GenBank) Reference ACC A8R0K3 PmId [17827660] Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation. (J Antibiot (Tokyo)….

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STAR+RSEM pippline without gtf

STAR+RSEM pippline without gtf 0 Dear all, I have question I mapped reads on cds sequence through STAR I don’t have gtf file and want to calculate read count using RSEM but I am stuck by error “RSEM error: RSEM currently does not support gapped alignments” as I don’t have…

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Which of the following is wrong about GenBank DNA Sequence Entry?

Which of the following is wrong about GenBank DNA Sequence Entry? (a) The information is organized into fields, each with an identifier, shown as the first text on each line (b) In some entries, these identifiers may be abbreviated to two letters, e.g., RF for reference (c) Some identifiers may…

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How to identify exon sequences

How to identify exon sequences 0 I’m trying to identify exons of a gene family from a genomic DNA. Initially, I’ve tried mapping the reference gene CDS to the genome to identify the exons. But then I won’t be able to obtain the UTRs and only the coding regions. So…

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ASM238634v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/05/2020 15:45:56 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,994 CDSs (total)::1,917 Genes (coding)::1,885 CDSs (with protein)::1,885 Genes (RNA)::77 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4,…

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X amino acid in ensembl

X amino acid in ensembl 2 Hello all, I am working on aligning proteins orthologs from different species. I am using the Ensembl API. Strangely, some protein sequences from non-human species have a lot of X. I wonder what does that mean? In theory, if their genome sequence is know,…

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How to rename the elements in columns(txdb)?

How to rename the elements in columns(txdb)? 0 Hello Biostars Community, I made a txdb object using: mm39.txdb <- makeTxDbFromEnsembl(organism = “Mus musculus”) and then made the CompressedGRangesList : txns <- GRangesList(cds(mm39.txdb, columns = c(“CDSSTART”,”CDSEND”))) I am trying to figure out how to rename CDSSTART to cdsStart and CDSEND to…

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Replace fasta header using bash : bioinformatics

Hello people, I got stucked with my new script and perhaps you can help me. Its goal is to take an input table with querys and subjects (originated by a local blast) and replace query names with subject names in the corresponding fasta file. In detail, the table input file…

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How to build a CompressedGRangesList with cdsstart/cdsend using custom txdb?

How to build a CompressedGRangesList with cdsstart/cdsend using custom txdb? 0 Hello Biostars Community, How do I build a CompressedGRanges List with cdsstart/cdsend in listData using a custom txdb using GenomicFeatures? I think this may be a simple GenomicFeatures task, but this is my first time doing this so I…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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gffread error

hello I am currently trying to do RNA-seq using public data in brassica juncea. To use htseq-count for making count table, I have to convert gff file which downloaded in brassica database to gtf file. So I used gffread for converting gff file with below command gffread Bju.genome.gff -T -o…

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Getting cDNA sequence from NCBI

Getting cDNA sequence from NCBI 1 I am looking at NCBI’s api page and I cannot seem to find any endpoint that returns the cDNA by transcript id. In fact NCBI nuccore has a webpage for this. and if I want to i can scrape the part coming after ORIGIN….

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Stref_00240 : CDS information — DoBISCUIT

Category 3.2 modification methylation Product putative O-methyltransferase Product (GenBank) O-methyl transferase Gene Gene (GenBank) stfMII EC number 2.1.1.- Keyword Note Note (GenBank) Reference ACC Q2P9Z1 PmId [16751529] Isolation, characterization, and heterologous expression of the biosynthesis gene cluster for the antitumor anthracycline steffimycin. (Appl Environ Microbiol. , 2006) comment steffimycin生合成gene clusterのクローニング、特徴づけ。 …

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Are there any alternatives to Liftoff

Are there any alternatives to Liftoff – Mapping annotations (GFF/GTF) between assemblies 2 Hi, I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1:…

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copper c19520 in rok

CHAPTER 4 COPPER AND COPPER ALLOYS – PDF Free Download 80 196 Copper and Copper Alloys Table 43 Velocity Guidelines for Copper Alloys in Pumps and Propellers Operating in Seawater UNS Alloy Number Peripheral Velocity ft/s m/s C C C90300 C C95200 C C95500 C95700 C Source: Copper Development Association….

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High-purity production and precise editing of DNA base editing ribonucleoproteins

Abstract Ribonucleoprotein (RNP) complex–mediated base editing is expected to be greatly beneficial because of its reduced off-target effects compared to plasmid- or viral vector–mediated gene editing, especially in therapeutic applications. However, production of recombinant cytosine base editors (CBEs) or adenine base editors (ABEs) with ample yield and high purity in…

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Sorting and writing multifasta entries to new fasta files

Sorting and writing multifasta entries to new fasta files 0 Hi, first post here. So I’m trying take the CDS out of various species’ orthologous sequences. I’m running on a Linux server, and am mainly aiming to use BioPython or Linux programs for this. I’ve run OrthoFinder on 28 species…

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ASM287662v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/10/2016 16:40:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,675 CDS (total)::3,608 Genes (coding)::3,557 CDS (coding)::3,557 Genes (RNA)::67 rRNAs::2, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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Mapping reads and quantifying genes

Mapping reads and quantifying genes – Metagenomic workshop 0 Hello, I am using the following metagenomic workshop tutorial to analyse my own metagenomic data. metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html I performed the following steps: mapped reads with bowtie2 and generated .bam file with samtools sort. Removed duplicates with picard Extracted gene information from prokka…

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Answer: PopGenome – VCF, fasta, GTF and codons still missing

Dear Maciek Hopefully you were able to solve these problems already. I cannot comment on the main set of issues you reported. However, I also encountered the error: `Error in START[!REV, 3] : incorrect number of dimensions` following certain instances of `set.synnonsyn` which I also noticed occurred for genes which…

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How to trim a GFF3 file based on specific coordinates?

How to trim a GFF3 file based on specific coordinates? 0 Hi, I would like to create a GFF3 file containing information only for specific coordinates from the chromosome level GFF3 file. I know how to extract gene and CDS info separately but don’t know how to do trimming based…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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STAR rna-seq for bacterial genomes

Hi, I’m willing to use STAR for bacterial genomes. I wanted to ask if this is strongly unadvised or if there is a way to manage the main challenges of mapping reads to prokaryotes. (I know there are specific tools for this purpose, i.e. EdgePro, but I’m a beginner in…

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