Tag: CDS

A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…

I downloaded Era5 single level data using Python, where I tried to calculate daily_means from hourly data prior to downloading. I read the returned NetCDF-file into RStudio using nc_file <- “path/download.nc” raster_data <- raster::brick(nc_file) This results in a LargeRasterBrick (with more than 5 million elements) of type S4. From here…

Lentiviral KCNT2 HUMAN sgRNA gene Knockout/Screening Kit -FenicsBIO The store will not work correctly when cookies are disabled. JavaScript seems to be disabled in your browser. For the best experience on our site, be sure to turn on Javascript in your browser. We use cookies to give you the…

I want to 1.) download and process wind data from the Era5 single layer cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=overview dataset using RStudio. The goal is to have a timeseries of several years of dailymean_windspeed (and direction) of an area (e.g. (57, 2, 51, 8). Calculating the daily means of u- and v- windcomponents prior…

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

How to run diamond blastp to get all vs all similarity score between proteins? 0 Hi. I have a .fa file representing multiple predicted proteins. Example: >NC_001341.1_1 # 397 # 714 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.314 MCSSSIISEKHLKKNIFQKKAKVQYKIKKNRRGQINENKCSINPNKKRSKKIKKLAKQKD IQACINIGNRYVDVPIRPVSVADPDTPKETKEDKEKGCHFRNGIH* >NC_001341.1_2 # 788 # 1009 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.306 MQCLISNEYHHNNNEHTSCINRINRNYRSNQRHHQGYNDLYDSINIIQGMLENLNASIVY FTKDGKYKLIMTL* Given this…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Hersbach, H. et al. ERA5 hourly data on single levels from 1940 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). In Copernicus Climate Change Service (C3S) Climate Data Store (CDS) (2023). doi.org/10.24381/cds.adbb2d47. Constable, A. J. et al. Cross-chapter paper 6: Polar regions. In Climate Change 2022: Impacts,…

Extract fasta sequence from gff3 file 2 Hi everyone, I have a lot of .gff3 files with the CDS features and below with the fasta sequence. This sequence is separated from the CDS features like this: ##FASTA >NZ_NZ_LR130533.1 I would like to extract all the fasta sequence into new fasta…

Renaming fasta files with their headers 1 Hi I have around 85 gene sequences in individual fasta files. I’d like to rename each file with their header name containing the gene name in [gene=]. For each header, I only want what is in-between the brackets. I’m trying to do this…

Weighted gene co-expression network analysis GSE131329 has comprehensive clinical data, and WGCNA was carried out with this expression profile. WGCNA is a systems biology method for characterizing gene association patterns between different samples, used to identify highly synergistic sets of genes and to screen for candidate biomarker genes or therapeutic…

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

how to run the compare_genomes for comparative analysis 0 Hi, I am interested to compare the 10 genomes for comparative analysis. I have genome, cds, protein and gff files for this analysis. I want to ask if someone has the experience of running the compare_genomes tool for this. I have…

How can I obtain the DNA sequences of each CDS for several genbank files? 0 Hello, I want to obtain DNA sequences of all the CDS from multiple genbank files in one fasta file. I tried several solutions with Biopython but nothing is working for me. I tried for exemple…

Convert NCBI Downloaded files to ANNOVAR format 0 I have been trying to understand from the ANNOVAR documentation and other sites the steps needed to make these files from NCBI available to ANNOVAR. I admit to being new to bioinformatics, but have been a software developer for 30+ years. My…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/05/2022 10:42:45 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,366 CDSs (total)::3,329 Genes (coding)::3,296 CDSs (with protein)::3,296 Genes (RNA)::37 tRNAs::34 ncRNAs::3 Pseudo Genes (total)::33 CDSs (without protein)::33 Pseudo Genes…

Now lets look at a flat file for delta globin and answer the following questions.   Go to the “Gene” data base, and search for “delta globin”. Choose the HBD link for human delta globin. Find the accession number NM_000519.3 under mRNA and protein. This will bring you to the mRNA…

datasets download genome accession –inputfile accessions.txt –include gff3,gbff,rna,cds,protein,genome,seq-report Or you simply specify mutliple accessions on the commandline: datasets download genome accession GCF_000001405.40 GCA_003774525.2 GCA_000001635 Edit: Sorry, I overlooked the –inputfile option. This is necessary unless all accessions are from a common taxon or bioproject. In the first case you can…

No matter how many thumb drives you have your college entrance essay backed up on, it won’t last forever. Electronics have a limited shelf life, so one company is turning to a data storage solution human beings have being using for as long as we’ve been around: DNA. Hard drives,…

. 2023 Nov 28:e202316007. doi: 10.1002/anie.202316007. Online ahead of print. Affiliations Expand Affiliations 1 Nanjing University, College of Engineering and Applied Sciences, CHINA. 2 Nanjing University, Medical School, CHINA. 3 Nanjing University of Chinese Medicine, School of medicine, CHINA. 4 Nanjing University, Biomedical Engineering, 22 Hankou Road, 210023, Nanjing, CHINA….

Viral metagenomic analysis The number of clean reads was 21,157,543 for the RNA sample and 26,789,502 for the DNA sample. For RNA, the data were assembled to a total sequence length of 2,337,534, with 60.92% GC content. The length of the largest contig was 11,556 nt, which was identified as…

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…

Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/19/2023 23:53:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::2,406 CDSs (total)::2,346 Genes (coding)::2,318 CDSs (with protein)::2,318 Genes (RNA)::60 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4, 4…

Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…

Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA 0 Dear Biostar Community I’m currently trying to generate a protein FASTA containing all known variants from HeLa (from Cosmic CellLinesProject) for variant detection in proteomics measurements. For this, I’ve downloaded the variants file (VCF) and the…

Tartt AN, Mariani MB, Hen R, Mann JJ, Boldrini M. Dysregulation of adult hippocampal neuroplasticity in major depression: pathogenesis and therapeutic implications. Mol Psychiatry. 2022;27(6):2689–99. doi.org/10.1038/s41380-022-01520-y Article  CAS  PubMed  PubMed Central  Google Scholar  Friedrich MJ. Depression is the leading cause of disability around the World. JAMA. 2017;317(15):1517. doi.org/10.1001/jama.2017.3826 Article  PubMed …

Working with NCBI downloadable Datasets 0 Hi all, I’m an postgraduate student currently working on an assigment in the field of “Analysis Molecular Data”. We’ve been instructed to examine polymoprhism in the promoter of the gene MMP3 in humans, and how that might affect expression and causality for genetic disorders….

Genome annotation (proving evidance from the RNA-seq raw reads) 0 Dear All, I have this question but need help answering it using the technical process (From mapping to quantification). I recently annotated a genome of eukaryotic species. So, After combining three methods using EvidanceModeler. The annotation of protein-coding genes yielded…

How to obtain full alignment results? 0 Hi, When I prepare to align my short reads to the human pan-genome graph genome, the result is only a path, 1. what I want is to provide me all the sequences that have a mismatch and full alignment with this reads? And…

Bedtools coverage -hist “all” in chr column 0 $ bedtools coverage -a A.bed -b B.bed -hist chr1 0 100 b1 1 + 0 70 100 0.7000000 chr1 0 100 b1 1 + 1 30 100 0.3000000 chr1 100 200 b2 1 – 1 100 100 1.0000000 chr2 0 100 b3…

Gene Synthesis in Metabolic Engineering The application of gene synthesis in the field of metabolic engineering is one of the most rapidly evolving areas within synthetic biology. This exciting research domain offers a wealth of potential economic benefits to industries seeking to develop efficient, practical, and cost-effective strategies for synthesizing…

Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…

In this problem, we will use Biopython to translate the CDS (CoDing Squence) sequence(s) in GenBank file. First, use the retrieve_GenBank_info(id) (from the lecture notw, also given below) to save the GenBank record of Helicobacter pylori 26695. id is the id of helicobactor you found in Problem 3. Make sure…

RefSeq: NC_003424 CDS #248 >NC_003424 (refseq) complement(join(604496..604959,605015..605355, /translatio MSSSSKDSSFQVETPVQNILETSTNSELQDQVSSPYEPDYNSPVKQAAASISALQTQDDT LFNNVDERTLENKDGNKSDDANFDQVSGIPSGSLEIPILNSATSNIRLTPSDTYNNIPVS DTNNEEISKNIYGAPILESTSSDFQSKDSLSTTQPSVSGGNGSTSQSPPSLDVEQNKPFS ISNEPVEQETENSSTKDLQVYDFQTASEHLPEQSLQNTTYYDPSKTYSSVNFEEIEYGKS HEKLDLPYRTTDFIPYSKDLSTSPEAHRTSIYSYSANLPNYYNEHNELHEHHNPQTPSSP ESAYSPENLQLNHEAQNVEYLGNNAAEKSLQMNLEDEQRFQQFLKDEESIMSNWYPGQFP SASRLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGN FVRGQKLHLEISKIQKKYQNQIENMKKGSHVTKSNQYSEMIGNLPYPTSSRKRTRSPLMS KGKSYDRKGSISMSKNFSPDCEILVTEDCPKEFVWGVEKVFQERRLNIHTTCLYRDSNLQ VIIKSCIINSVKSIILINAGLAHLGKVSVQVFKDGSSDSEVRCDEYAAVDVMVAASIVHH AKTSLMHSAASSTPSYNGERIVPDVPSPCISTNPNLPALVGSLDSVNLHHLLGFIQNTYS TTSYIPTRVSFNPNDTGGSFGTITSQSQFVVNEMPKNYARDNYEALHSQESRQRSSVAGN KQLQKILEQLAELKQPDF BLAST Read more here: Source link

RefSeq: NC_010943 CDS #580 >NC_010943 (refseq) 628606..629976 /translation= MPIHSSVLELIGQTPIVKAQRLDTGVCELYLKLESANPGGSIKDRIGLSMIEAAEQRGDL KPGATLVEGTAGNTGLGLALVAQQKGYKLILVVPDKMSREKIFNLKAMGAEVRLTRSDVA KGHPEYYQDLAKTIAEQTPGAYFINQFGNPDNPAAHEFGTGPEILEQMGGDLDAIVFGCG SSGTMTGLSRAFAKLSPKTELVLADPVGSILAEYINDGVLNDKSGSWLVEGIGEDFLPSI SDFSRVKKAYAISDAESFHTARELLGKEGILGGSSTGTLLAAALKYCKEQTTPKKVLVLV CDTGNKYLSKMYNDYWMLDNGFLERPQHGDLRDLILRPYGQRDTVVIGPNDLLTTAYQRM KLYDVSQLPVMDGDQLVGIVDESDVLLHVYGDEARFRDTVATAMVSKLDRLDVKSPIEAL LPVFDRGQVAIVMDGNAFLGLITRIDLLNYLRRRVQ BLAST Read more here: Source link

RefSeq: NC_001134 CDS #316 >NC_001134 (refseq) 625772..628309 /translation= MSAALPSIQLPVDYNNLFNEITDFLVTFKQDTLSSDATRNENEDENLDAENIEQHLLEKG PKYMAMLQKVANRELNSVIIDLDDILQYQNEKFLQGTQADDLVSAIQQNANHFTELFCRA IDNNMPLPTKEIDYKDDVLDVILNQRRLRNERMLSDRTNEIRSENLMDTTMDPPSSMNDA LREVVEDETELFPPNLTRRYFLYFKPLSQNCARRYRKKAISSKPLSVRQIKGDFLGQLIT VRGIITRVSDVKPAVEVIAYTCDQCGYEVFQEVNSRTFTPLSECTSEECSQNQTKGQLFM STRASKFSAFQECKIQELSQQVPVGHIPRSLNIHVNGTLVRSLSPGDIVDVTGIFLPAPY TGFKALKAGLLTETYLEAQFVRQHKKKFASFSLTSDVEERVMELITSGDVYNRLAKSIAP EIYGNLDVKKALLLLLVGGVDKRVGDGMKIRGDINVCLMGDPGVAKSQLLKAICKISPRG VYTTGKGSSGVGLTAAVMKDPVTDEMILEGGALVLADNGICCIDEFDKMDESDRTAIHEV MEQQTISISKAGINTTLNARTSILAAANPLYGRYNPRLSPLDNINLPAALLSRFDILFLM LDIPSRDDDEKLAEHVTYVHMHNKQPDLDFTPVEPSKMREYIAYAKTKRPVMSEAVNDYV VQAYIRLRQDSKREMDSKFSFGQATPRTLLGIIRLSQALAKLRLADMVDIDDVEEALRLV RVSKESLYQETNKSKEDESPTTKIFTIIKKMLQETGKNTLSYENIVKTVRLRGFTMLQLS NCIQEYSYLNVWHLINEGNTLKFVDDGTMDTDQEDSLVSTPKLAPQTTASANVSAQDSDI DLQDA BLAST Read more here: Source link

RattusnorvegicusBRCA1mRNA,completecds GenBank:AF036760.1 GenBankFASTA LinkToThisView|Feedback F5001K1,5002K2,5003K3,5004,500SKS,Sm £AF036760.1 ~|Find: ME=I=4[oNI] @AEE< ATools+|¥Tracks +¥,Download»&7′~ lISBB[lK11,580l2KlZ,SOBPKP‘SPQ“K_IiSBBISK5,607 | 208x SI –—>_ rINGIRBRCT_assoc=0AAAC36493.1secTB3ercTI HHCDS:AAC36493.1PM fFros-: Name:BRCA1 | D‘:mermter”uce[pol… Location:118..5,571 Dimerinterface[pol [Length] BRCT sequencemotiff SEanon AF03676 BRCTsequencemotifI 1[se@[tk|1.50013Proteinlength:1,|4.500[sK5,607 AF036760.1:1..5.6K(5,607nt)[PositionalInfo] AF036760.1position:1,950CDSposition:1,833 Proteinposition:611 Proteinsequence:HSSKAPKKNRLRRKS[T]RCVLPLEPISRNPS DownloadFASTA:AAC36493.1 Links&Tools BLASTProtein:AAC36493.1 BLASTnr:AF036760.1(118..5,571) BLASTtoGenome:AF036760.1(118..5,571) AAC36493.1 FASTArecord:AF036760.1(118..5,571) AAC36493.1 GenBankrecord:AF036760.1(118..5,571) AAC36493.1 GraphicalView:AAC36493.13°Tracksshown:2/3 Read more here: Source…

Job:Bioinformatics Research Associate, Genomics and Genetics 0 @jp-carter-15371 Last seen 7 hours ago Nashville, TN The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing…

Job:Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics 0 @jp-carter-15371 Last seen 3 hours ago Nashville, TN Creative Data Solutions (Vanderbilt University, Nashville, TN, USA) is seeking a Bioinformatics Research Associate, who will be involved in a variety of life sciences projects and be directly involved in workflows and pipelines…

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is rather strange (mainly the INFO column). ##VEP=”v108″ time=”2023-04-27 15:13:08″ cache=”workflow/resources/variants/cache_vep/homo_sapiens/108_GRCh38″ ensembl-funcgen=108.56bb136 ensembl-variation=108.a885ada ensembl-io=108.58d13c1 ensembl=108.d8a9c80 1000genomes=”phase3″…

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

Sorry if this question comes across as too basic. I am trying to understand the mRNA molecule storage in genbank. Here is the link: www.ncbi.nlm.nih.gov/nuccore/NM_001344249.1?report=genbank&to=1894 Now the literature says that for mRNA, the corresponding cDNA is submitted to NCBI database. But when I go through the content of this link,…

Matching protein IDs starting with WP_ to protein IDs starting with YP_ 0 Hi all, I have annotated genomes where all CDS have protein IDs starting with YP (e.g., YP_005225157.1). Is there a way to automatically convert protein IDs that start with YP to those starting with WP, without the…

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

I am looking for a way to do the following 1) reliably find a protein structure e.g. pdb file or pre-computed alphafold results that is associated with a particular gene/transcript isoform. I found a way to do this somewhat for human genes using biomart, but i’d like to be able…

How to make a proteome file 0 I have the fasta files and genome annotation (gff) files for a number of species, and I am now trying to create proteome files for these species. I have tried extracting and translating only CDS sequences, and also only protein-coding gene sequences, however…

Monocle3 transition to seurat 1 I know to transition from Seurat to monocle3 one has to use library(Seurat Wrappers) and then use the function: as.cell_data_set(seuratobject). But, after reclustering in monocle3, i would like to go back to Seurat to perform differential analysis. How do i do this? How do i…

Job DescriptionThe Cancer Data Science (CDS) team at the Broad (www.cancerdatascience.org/) is an interdisciplinary group dedicated to accelerating cancer research. We help design and analyze large-scale experiments, develop new statistical tools and machine learning methods, write papers, produce datasets used by tens of thousands of researchers around the world, and…

ExGenbank-new-answers From 22111 Note: numbers in Part 2 and Part 3 are updated on February 7, 2022. Part 1 QUESTION 1.1 a) Inspecting the FEATURE table of the entry reveals that two CDS regions are defined; therefore there are two genes in this entry. As stated on the GenBank hand-out…

Monocle3 garnett 0 I am trying to annotate my cells using garnett, but i keep getting this error at this stage. Error: is(object = cds, class2 = “CellDataSet”) is not TRUE. Here is my code: library(garnett) library(org.Mm.eg.db) classifier <- readRDS(“./mmLung_20191017.RDS”) trac <- classify_cells(trac, classifier, db = org.Mm.eg.db, cluster_extend = TRUE,…

Use case: We have an application built on CAP Java and unlike traditional CAP structure we have implemented RestController for consuming data from SAP Event Mesh queue using webhook. To develop and describe this api we wanted to implement Swagger. Our CAP App is on Springboot 3.* and we have…

Custom-made, ready-to-use iLenti™ and iLenti™-GFP siRNA constructs for transfection or infection to knockdown your gene of interest Services for a single construct or 4 constructs Guaranteed knockdown for any gene* Constructs available with a GFP reporter Full service at very low cost *Requirements: Only for siRNAs designed against human, mouse,…

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

Transcribed image text: The Structure And Sequence Of The Human BetaGlobin Gene The sequence below is the sequence of the human beta-globin gene from chromosome 11 . This particular version of the beta-globin gene’s sequence is from the National Center for Biotechnology Information’s GenBank database. GenBank is the repository for…

Genome assembly and annotation Each genome was assembled following a reference-based strategy. To that end, the reads from each sample were trimmed by quality. Phred quality scores before trimming were greater than Q30 (Additional file 1: Table S1) for all samples. Quality-trimmed reads from the Peruvian and Mexican isolates were…

Findings from the genomics field have slowly started to find applications in clinical care. The field of “genomic medicine” could potentially improve patient health and treatment strategies or better predict the likelihood of disease. The IGNITE demonstration projects, funded through the National Human Genome Research Institute (NHGRI), incorporate genomic information…

LOCUS XP_024590519 142 aa linear MAM 18-APR-2018 DEFINITION glia maturation factor beta isoform X2 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024590519 VERSION XP_024590519.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024734751.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria;…

Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…

LOCUS XP_033346483 290 aa linear INV 16-APR-2020 DEFINITION COP9 signalosome complex subunit 7b isoform X1 [Bombus vosnesenskii]. ACCESSION XP_033346483 VERSION XP_033346483.1 DBLINK BioProject: PRJNA623919 DBSOURCE REFSEQ: accession XM_033490592.1 KEYWORDS RefSeq. SOURCE Bombus vosnesenskii ORGANISM Bombus vosnesenskii Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila;…

Dataset’s name in BioMart for S. pombe 2 Can anybody help me to find the dataset for s. pombe on BioMart? And also some help on how to use makeTranscriptDbFromBiomart to create TranscriptDB? cheers, S.pombe BioMart dataset • 3.6k views Looks like you figured out another way of getting what…

Violin plot (Monocle 3) – Troubleshooting 0 I am trying to generate some violin plots in monocle on a cell dataset object. Basically, I’m trying to visualize expression of certain marker genes in different clusters of a cell dataset object. I tried to follow this online documentation using the plot_genes_violin…

How to download genomes and proteins from JGI in bulk via the command line? 0 I’m trying to figure out how to download from JGI in bulk. In particular, I’d like to grab the genome and MycoCosm (mycocosm.jgi.doe.gov/). I honestly have no idea where to start. I see that there…

Download the GENCODE human genome annotation version Release 44 (GRCh38.p14) using the following link: GFF3 Write R code to perform each of the following tasks. 1. Numbers of genes on each chromosome Visualize using bar plot (function barplot()) the total number of genes on each chromosome (1-22, X, Y). Report…

1)Which of the following statements about introns in the human genome are incorrect? (Choose all answers that apply. 4 pts a)For protein-coding genes, only the exons are transcribed into mRNA (Note: introns are also transcribed, but removed in mature mRNAs) b)The average length of introns in the human genome is…

Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…

What is wrong with my NCBI esearch command for 16S rRNA? 0 Hi there, I am trying to extract the 16S rRNA from my genomes using the genome accession from NCBI. I tried the code below and ended up with the same unrelated sequence for each of my accessions. Instead…

There is nothing wrong with these files. Sort (as any GTF): zcat Homo_sapiens.GRCh38.105.gtf.gz \ | awk ‘$1 ~ /^#/ {print $0;next} {print $0 | “sort -k1,1 -k4,4n -k5,5n”}’ \ | bgzip > Homo_sapiens.GRCh38.105_sorted.gtf.gz That having said, if you need the file being strictly coordinate-sorted then you always have to do…

I have discovered that my gff3 file is not in order at the time of defining the gene, mRNA and CDS. An example LG1 phytozomev10 gene 10835748 10846741 . – . ID=gene00257-v1.0-hybrid.v1.1;Name=gene00257-v1.0-hybrid LG1 phytozomev10 mRNA 10835748 10846741 . – . ID=mrna00257.1-v1.0-hybrid.v1.1;Name=mrna00257.1-v1.0-hybrid;pacid=27244575;longest=1;Parent=gene00257-v1.0-hybrid.v1.1 LG1 phytozomev10 CDS 10846566 10846741 . – 2 ID=mrna00257.1-v1.0-hybrid.v1.1.CDS.1;Parent=mrna00257.1-v1.0-hybrid.v1.1;pacid=27244575…

Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…

Sample collection and DNA extraction An individual E. imbricata was obtained from the sea turtle rescue base on Naozhou Island, Zhanjiang City, Guangdong Province, China. A 10 mL blood sample was drawn from its jugular sinus and rapidly frozen for further analysis. Genomic DNA was extracted from the processed blood samples…

Phenotypic characteristics of K. bulderi strains at low pH, organic acids, and antimicrobial drugs Since K. bulderi was isolated, only two studies have been conducted to investigate its physiological characteristics (7, 8). This species was shown to be able to grow efficiently at low pHs ranging from 5.0 to 2.5…

What does a gene’s “aligned length” represent? 0 What does a gene’s “aligned length” represent in the NCBI gene database? I can understand that CDS length represents the length of the coding sequence (the number of amino acid residues + 1 and then multiplied by 3), but I really can’t…

Clinical samples and plasma preparation Blood samples from control individuals and patients with multiple myeloma, liver cancer, and lung cancer were obtained from Oregon Health and Science University (OHSU) by Knight Cancer Institute Biolibrary and Oregon Clinical and Translational Research Institute (OCTRI). All samples were collected under OHSU institutional review…

LOCUS XP_007448290 260 aa linear MAM 01-APR-2014 DEFINITION PREDICTED: alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 isoform X1 [Lipotes vexillifer]. ACCESSION XP_007448290 VERSION XP_007448290.1 DBLINK BioProject: PRJNA232751 DBSOURCE REFSEQ: accession XM_007448228.1 KEYWORDS RefSeq. SOURCE Lipotes vexillifer (Yangtze River dolphin) ORGANISM Lipotes vexillifer Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla;…

I am validating a flatfile of an annotated chloroplast genome scaffold. It includes /organism=”Cannabis sativa” and /organelle=”plastid:chloroplast”. This means the CDS should be translated according to the bacterial translation table and I therefore included the /transl_table=11 qualifier in my CDS annotations. See head of of the flatfile below (some info…

LOCUS XP_026912832 160 aa linear MAM 04-APR-2023 DEFINITION protein FAM162B isoform X3 [Acinonyx jubatus]. ACCESSION XP_026912832 VERSION XP_026912832.1 DBLINK BioProject: PRJNA923316 DBSOURCE REFSEQ: accession XM_027057031.2 KEYWORDS RefSeq. SOURCE Acinonyx jubatus (cheetah) ORGANISM Acinonyx jubatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Acinonychinae; Acinonyx. COMMENT MODEL…

Isolation and identification of E. marmotae M-12 The M-12 isolate was obtained from the lungs of a male bank vole (Myodes glareolus). Culture M-12 was stored in NB with 15% glycerol at − 80 °C. Microscopy investigation revealed a single Gram-negative coccobacillus in M-12 isolate. Catalase-positive and oxidase-negative reactions were observed. Isolate…

LOCUS NP_001154929 155 aa linear ROD 03-MAY-2023 DEFINITION core-binding factor subunit beta isoform 3 [Mus musculus]. ACCESSION NP_001154929 VERSION NP_001154929.1 DBSOURCE REFSEQ: accession NM_001161457.1 KEYWORDS RefSeq. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus;…

LOCUS XP_007166569 140 aa linear MAM 27-JUN-2023 DEFINITION profilin-1 [Balaenoptera acutorostrata]. ACCESSION XP_007166569 VERSION XP_007166569.1 DBLINK BioProject: PRJNA986088 DBSOURCE REFSEQ: accession XM_007166507.3 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata (minke whale) ORGANISM Balaenoptera acutorostrata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera. COMMENT MODEL REFSEQ:…

LOCUS XP_024597028 208 aa linear MAM 18-APR-2018 DEFINITION protein THEM6 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024597028 VERSION XP_024597028.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024741260.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Odontoceti;…

LOCUS XP_013985108 229 aa linear VRT 07-JAN-2022 DEFINITION esterase OVCA2 isoform X1 [Salmo salar]. ACCESSION XP_013985108 VERSION XP_013985108.1 DBLINK BioProject: PRJNA788898 DBSOURCE REFSEQ: accession XM_014129633.2 KEYWORDS RefSeq. SOURCE Salmo salar (Atlantic salmon) ORGANISM Salmo salar Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo. COMMENT…

I’m analyzing the WES data of a patient, after calling variants by GATK, I use Ensembl Variant Effect Predictor (VEP) to annotate my vcf file. Here is one record from the output file: #Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra chr11_64341844_GTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT/- chr11:64341844-64341923- ENSG00000278359…

Getting CDS 5’/CDS3′ incomplete flags info from ENSEMBL using biomaRt 0 @alioghabian-8516 Last seen 10 hours ago Finland Hi ! I was wondering how I can get (In R) the ENSEMBL ID of all transcripts that have been flagged with “CDS 5′ incomplete”, “CDS3′ incomplete” and “CDS 5′ and CDS3′…

RefSeq: NC_014103 CDS #2688 >NC_014103 (refseq) complement(2757269..2758306) /translation= MGNSYNTIVIGAGQAGLAIGYYLKQKSLSFLIIDSNSRVGDSWRHRYDSLILFTPRSHSA LPGMNVEGSPHGYPNKDEIADYLENYSRHYNLPVQLNTAVINLFKENEQFHLVTNKGNYV AKNIVVATGPFQKPFVPDVEKDVLKDIFQIHAAHYKNPTQLNEGTTLIVGAGNSGVQIAT ELAESREVYLSVGKRMKFLPYTLLNRSVFWWFQVLGLSKATIHSKLGQFMKKNDPIIGKE LKPLLSRGVVKKVSKVSKADGKSLICQNGEKVQPKNIIWATGYHNDYEWIEIPNIIDKNN NVIHDRGITKEKGLYFLGLSWQYRRGSALLLGVGEDAKFLANHIT BLAST Read more here: Source link

GenBank: GU117629 CDS #6 >GU117629 (genbank) 3689..5254 /translation= MSNIPRKRAKRDSATHLYQQCQISGNCPEDVKNKIEGTTLADKLLKILSSIVYFGGLGIG TGKGSGGSYGYRPLGGGGGGGARVTGDGTVIRPSIVVEPVGPSDIIPIDALSPSSSSVVP LAEAGPELVIPDTVPDLGAGEIEVIAEPDTIEVSGSETVPTISSTDDNAAVIDVQSPIPT PRRVTSTSRFSNPSFVSIVTTSSTSDIAAEGATAINVFVDAAAGGETIGEEIPLIDLNEI QEFQIDEPAQPRSSTPLAFQRAFSRAREPYNRRVRQVMTRNTDFLTRAPQAVQFDFENPA FQNDVTIEFEQDLNQLAAAAPDPDFADIVKLRRPIFSETPQGNIRVSRLGTKGTIKLRSG TQIGETIHFYYDLSSIENAEAIELSVLGEHSGDATVINPIAEGTFVDAENGEVPLLFPDE ELLDDVTEDFSNSHVILSSSSRRSVVSVPTLPPGVALKVFIDDVGKGLFVSYPISYESIP ENYIPATDDIPSILIDGFSSDDFVLHPSHSRKRRRKRTPLL BLAST Read more here: Source link

LOCUS XP_018454631 269 aa linear PLN 08-JUN-2023 DEFINITION disease resistance protein ADR2 [Raphanus sativus]. ACCESSION XP_018454631 VERSION XP_018454631.1 DBLINK BioProject: PRJNA344915 DBSOURCE REFSEQ: accession XM_018599129.2 KEYWORDS RefSeq. SOURCE Raphanus sativus (radish) ORGANISM Raphanus sativus Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus….

The question was asked before in Calculate CDS phase in gff3 format ; Negative value in “phase” line of a gff3 file.What does it mean? ; etc… but I still don’t get it. So let’s use an existing GFF3 file: github.com/samtools/bcftools/blob/develop/test/csq/ENST00000580206/short.gff The GFF3 is valid in ‘bcftools csq’ This is…

build databses for genome using snpEff 1 hello, please i got this error when i try building a database for date plam genome Total: 363391 markers added. Create exons from CDS (if needed): …………………………………………………………+………………………………………………………………………………………………………. Exons created for 138 transcripts. Deleting redundant exons (if needed): Total transcripts with deleted exons: 0…

RefSeq: NC_016460 CDS #712 >NC_016460 (refseq) join(2698549..2698569,2698649..2698669,2698741..2699330, / MATTVEKIKEIEAEMARTQKNKATSYHLGQLKAKLAKLKRELLTPSGGGGGGGGVGFDVA RTGVASIGFIGFPSVGKSTLMSRLTGQHSEAAAYEFTTLTSVPGQVIYNGAPLQMIDLPG IIEGAKDGRGRGRQVIAVAKTCHLIFIVLDVNKPLTDKRIIESELEGFGIRINKEPPNIT FRKKDKGGLNITSTVPLTHIDHDEIRAVMSEYKISSADITIRCDATIDDLIDVLEAKSRS YIPVIYVLNKIDSISIEELDLLYRIPNAVPISSEHGWNIDELMEAMWEKLNLIRVYTKPK GKMPDYSAPVVLRASKCTVEDFCNAIHRSIVDQFKTAIVYGKSVKHQPQRVGLSHELADE DIVTIVKK BLAST Read more here: Source link

efetch from NCBI E-utilities returns “curl error s 400 & 500” and takes a very long time 0 I run this command to download ~4,000 gene sequences for invA gene for taxonomy# 28901. It works fine for smaller datasets, but … but takes very long time and never finishes for…

RefSeq: NC_018012 CDS #1958 >NC_018012 (refseq) 2162410..2163444 /translation= MLKQFDALPDGLLDAESHQLNAWLGAPTLIHLSGAREPALFVSVLMHGNETVGWDAIRNL LQARLARFGESRLPRSLTIFIGNVAAAASSARHLPEQPDYNRVWPGSVTPHTPEHDIMAR VVEIMAERRLFASLDLHNNTGSNPHYACIDQIDNRILQLATLFSRTVVYFKRPTGVQSMA MARLCPAVTVECGKVGEQHGIEHARNFIDAALHLNDIPDHALPAQDIDLFHSVAQVTVPA EVRFSFSSDEVDLLLNPALEHWNFCELPRGTAFGRRLNGKAARLEVRDEQGLDVSERYFH AEDFELRLRQPAMPSMLTRDETVIRQDCLCYLMERYREHLPQRN BLAST Read more here: Source link

Mouse models C57BL/6J (strain 000664, The Jackson Laboratory) and B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*/-EGFP)Fezh/J (strain no. 026179, The Jackson Laboratory) were used for all experimental procedures. The Npm1c/Flt3-ITD/Cas9 model has been extensively described previously31,57,58. The maximal tumor size allowed by the Home Office license for this project and authorized by the Animal Welfare Ethical…

RefSeq: NC_007761 CDS #32 >NC_007761 (refseq) complement(34157..35557) /translation= MSTEKDYVVADIGLADFGRKEITIAETEMPGLMSCRAEFGEAKPLKGARITGSLHMTIQT AVLIETLVALGAEVRWASCNIFSTQDHAAAAIAAAGVPVFAIKGESLEDYWVYTDKIFQW ADGGLSNMILDDGGDATMYILLGARAEAGEDVLSNPHSEEEEILFAQIKKRLAASPGWFT KQRDAIKGVTEETTTGVNRLYQLSQKGLLPFPAINVNDSVTKSKFDNKYGCKESLVDGIR RGTDVMMAGKVAVVCGYGDVGKGSAASLSGAGARVKVTEADPICALQAAMDGYEVVLLED VVSSADIFITTTGNKDVIRIDHMRQMKDMAIVGNIGHFDNEIEVAALRNLKWTNVKPQVD LIEFPKGNRIILLSEGRLLNLGNATGHPSFVMSASFTNQTLAQIELFTKPGQYENKVYIL PKHLDEKVARLHLDKLGVKLTQLSEEQAAYIGVKPQGPFKSDHYRY BLAST Read more here: Source link

RefSeq: NC_010681 CDS #662 >NC_010681 (refseq) 733931..734860 /translation= MKPIPPLTALRCFEAVARLGGVTQAARELHVTHSAVSQQIKVLEDSMGVALFMREARGLR LTEEGRLYALDIRMALRDIAHATRRAQARPHESELVITTLPSFAQHWLVPRLGSFRDAHP YYRIRLQTSLQVEDFRLGASDIGIRMGQGHWPNVAQQKLFDDEMVVVAAPHFALTHGRLP SNAAEVLACPLISSPDTPWHDWCQAAQVAEPAEGAVVLSANDSNIVIGAVLLGQGIALER RSLVAYALARGELVQITDIRVPYRYPYWLVWQQRDMLNASQAHFAQWIEGQVDTYLRSSN APAAALRAG BLAST Read more here: Source link

RefSeq: NC_022040 CDS #2057 >NC_022040 (refseq) complement(2261426..2262451) /translation= MSVTNFRRFLAGIAVIAACVAATPTAQAQSSGSSGSSGSSAGSSGLWDLLFPESHESFIE RLLDPLDDSHISIHPDLTPDLYEEVFDPPQIGECPAVVAVVARGSEQNLQIRPARYSEES PWTSNGFEEKNFRSFFGRMEKHYRESTGESLMKDVYVMGLNNIEYPASLPLSSEGSSAIE LGTSISSGRDNVISAIDRFESATGCTPKYLLAGYSQGVLIVDGYEEELIARDQYLGTLHI ANPAQQVDDPTLVGHEVTTGGLASSVEPVEDNPFKVSYCLPGDIVCDRSFEQFSAAGSSI AAAQLSTGNIRPGRVHVQYFVTTQPWDEQIFDEVASWIEAA BLAST Read more here: Source link

Findings from the genomics field have slowly started to find applications in clinical care. The field of “genomic medicine” could potentially improve patient health and treatment strategies or better predict the likelihood of disease. The IGNITE demonstration projects, funded through the National Human Genome Research Institute (NHGRI), incorporate genomic information…

Error in h(simpleError(msg, call)) in monocle2 0 Want to run monocle2 for a single cell RNAseq data processed using Seurat, but encountering following problem. library(monocle) Seurat An object of class Seurat 41445 features across 55683 samples within 1 assay Active assay: RNA (41445 features, 1850 variable features) 4 dimensional reductions…