Tag: ncbi

Taxonomic and molecular characterization of a new entomopathogenic nematode species, Heterorhabditis casmirica n. sp., and whole genome sequencing of its associated bacterial symbiont | Parasites & Vectors

Six populations of Heterorhabditis nematodes (HM, HM8, HP1, HPH, HH1, and HH4) were isolated from agricultural soils in Kashmir, India. Initial molecular and morphological characterization showed that they are genetically identical, morphologically very similar, and represent a novel species closely related to H. bacteriophora. The nematode population HM was chosen…

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Mapping .fna reference genome to itself in order to include it as an outgroup

Mapping .fna reference genome to itself in order to include it as an outgroup 0 Hello, Please pardon a potentially naive question. I have 30 newly sequenced WGS data files for a bird species.These are all in a FASTQ format. I have mapped them to a reference genome from NCBI,…

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Bioinformatic Analysis of circRNAs in Human ASO

Introduction Arteriosclerosis obliterans (ASO) is a chronic disorder with atherosclerosis involving lower extremity arteries leading to arterial stenosis or occlusion. The incidence continues to increase with age, affecting about 202 million people worldwide to varying degree.1–3 Despite the proposed theories of lipid infiltration, arterial intimal injury, and chronic inflammation, the…

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How to make a proteome file

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…

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Roche enters into a definitive agreement to acquire Telavant including rights to novel TL1A directed antibody (RVT-3101) for the treatment of inflammatory bowel disease from Roivant

Roche will gain the rights to develop, manufacture and commercialise RVT-3101 in the US and Japan for the treatment of inflammatory bowel disease and potentially multiple other diseases RVT-3101 is a Phase 3-ready antibody with first-in-class and best-in-disease potential, a novel mode of action and strong Phase 2b data in…

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GPP Web Portal – Gene Details

Gene: Human LOC642131 (642131) immunoglobulin IGHV1OR15-3-like pseudogene Source: NCBI, updated 2019-09-11 Taxon: Homo sapiens (human) Chromosome: 15 Wildtype Transcripts: NR_135667.1 Additional Resources: NBCI Gene record: LOC642131 (642131) NCBI Gene records for discontinued versions of this gene: LOC102724835 (102724835) sgRNA constructs originally intended to target this gene (CRISPRko, NGG PAM) NOTE:…

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BLAST database error

BLAST database error 1 Hello, For my project I downloaded blast+ executables and also a database using this: perl ../ncbi-blast-2.14.1+/bin/update_blastdb.pl –passive –decompress nt_euk.01 Then I tried to extract fasta sequence from this nt_euk.01 database using this command: blastdbcmd -entry all -db nt_euk.01 -out nt_euk1.fasta But it gave me this error:…

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Identification of novel and known miRNAas using mirdeep2 in galaxy – transcriptomics

Hello everyone,Im cureeently working on miRNA data and i need to know the known and novel mirnas present in my samples. im using mirdeep2 for mapping and quantification. Here mirdeep2 is asking input files colapse and maaped files which i have provided it which i got via mirddep2 mapper and…

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SNP Genotyping Market – Size, Share, Trends

The Business Research Company’s Single Nucleotide Polymorphism (SNP) Genotyping Global Market Report 2023 is the most detailed report available on the market, including broad forecast periods and multiple geographies. The report covers the historic period – 2010-2021, and the forecast period – 2023-2032. The Single Nucleotide Polymorphism (SNP) Genotyping Global…

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proteins will bind to the column you used based on

proteins will bind to the column you used based on working pH of 6.0.1. Use the website www.ncbi.nlm.nih.gov/: proteindatabase>>search>> Whey protein by name >>scroll down through citedreferences to see amino acid sequence or look at FASTA format to seesequence.2. Copy amino acid sequence of interest intoweb.expasy.org/compute_pi/ to compute MW and…

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Can I still remove ambient RNA if I do not have raw barcode-gene matrix?

Can I still remove ambient RNA if I do not have raw barcode-gene matrix? 0 Hi, I would like to use SoupX for ambient RNA removal. However, I am using barcode-gene matrix datasets downloaded from NCBI GEO which don’t always include raw data. Can I still use SoupX without the…

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The Biostar Herald for Monday, October 23, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle

doi: 10.1186/s13567-023-01227-0. Affiliations Expand Affiliations 1 Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany. 2 Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany. 3 Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences,…

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Eukaryotic Genome Annotation | Genome Annotation Pipeline

PASAPASA was originally developed at The Institute for Genomic Research in 2002 as an effort to automatically improve gene structures in Arabidopsis thaliana. Since then, it has been applied to numerous Eukaryotic genome annotation projects including Rice, Aspergillus species, Plasmodium falciparum, Schistosoma mansoni, Aedes aegypti, mouse, human, among others. Functions of PASA…

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EMDB < EMD-25228

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Adversarial and variational autoencoders improve metagenomic binning

Overview of AAMB The AAMB workflow consists of the following main steps (Fig. 1a). First, Tetra Nucleotide Frequencies (TNF) and per sample co-abundances (Coab) are extracted from the contigs and BAM files of reads mapped to contigs, and input to the AAMB model as a concatenated vector. The AAMB model encodes…

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Structure of human TRPM8 channel

Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…

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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership | Genome Biology

Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…

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How difficult is it to set up local BLAST?

How difficult is it to set up local BLAST? 1 Hello! I hope that you are doing well. I have an application that needs to perform BLAST searches. I initially was intimidated by setting up BLAST+ on my local machine. So, instead I tried to use BioPython and BLAST+ to…

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How To Blastguide – guide of using blast tool – NCBI Handout Series | BLAST homepage & search

NCBI Handout Series | BLAST homepage & search pages | Last Update December 20, 2019 Contact: blast–help@ncbi.nlm.nih.gov BLAST Homepage and Selected Search Pages Introducing the BLAST homepage and form elements/functions of selected search pages blast.ncbi.nlm.nih.gov National Center for Biotechnology Information • National Library of Medicine • National Institutes of Health…

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Remote BLAST search

Remote BLAST search 2 Hello all! I hope you are doing well. I have a program that needs to make BLAST requests. However, all of the methods that I have tried are dreadfully slow. I have tried using BioPythons NCBIWWW as well as remote BLAST+, but both are horrendously slow….

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Proper HTSeq usage on bacterial genome. Don’t quite understand –t

Proper HTSeq usage on bacterial genome. Don’t quite understand –t 1 Hi everyone, I’m trying to run HTSeq on a group of BAM files generated from the alignment of an RNAseq illumina reads mapped to a reference genome. The reference genome is the sequence with highest quality available and was…

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Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Cloning Supplementary Table 1 shows the synthetic gene, DNA and RNA oligonucleotide sequences used in this study. The synthetic genes encoding B.fragilis Cas6, CorA, NrN and C. botulinum SAM lyase purchased as g-blocks (IDT) were codon-optimized for expression in E. coli C43 (DE3) via the vector pEhisV5TEV, which encodes eight…

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BioSpace hiring Advisor/Sr. Advisor – Bioinformatics in Cambridge, MA

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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Bioplastic (poly-3-hydroxybutyrate)-producing Massilia endophytica sp. nov., isolated from Cannabis sativa L. ‘Cheungsam’

Sample collection and bacterial isolation The strain DM-R-R2A-13T was obtained from a sample of Cannabis sativa in Andong, Republic of Korea. To isolate the strain, leaf samples (5.3 g) and root samples (6.3 g) were subjected to surface-sterilization using 1% sodium hypochlorite for 20 min followed by 70% ethanol for 10 s, and then…

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Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…

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Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system

Uncultured microorganisms constitute a significant proportion of microbial populations in an ecosystem and play a vital role in its functioning1. The challenges associated with cultivating these microbes have constrained access to the vast phylogenetic and functional diversity they possess. However, recent advancements in metagenomics have opened a new window to…

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How to determine the conserved regions in the genome assembly

How to determine the conserved regions in the genome assembly 0 Hi, I have identified some tandem repeat loci from the reference assembled genome of a fungal species, and now I want to screen for loci located near conserved regions. How can I determine the conserved regions? There are three…

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Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

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Generating Positional List from VCF

I think one of the ways to achieve your goal is by converting your VCF file to a MAF (Mutation Annotation Format) file. To this end, you may want to check out the fuc package I wrote: >>> from fuc import pyvcf, pymaf >>> data = { … ‘CHROM’: [‘chr1’,…

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How to use efetch to download genome/proteome/etc. at the command line?

How to use efetch to download genome/proteome/etc. at the command line? 1 Use NCBI datasets tool for this type of workloads (LINK) datasets download genome accession GCF_000146045.2 –include rna Login before adding your answer. Traffic: 1457 users visited in the last hour Read more here: Source link

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Comparative study on the mutation spectrum of L-MYC and C-MYC genes of blood cfDNA in patients with ovarian cancer and healthy females

doi: 10.1111/jog.15808. Online ahead of print. Affiliations Expand Affiliations 1 Centre for Interdisciplinary Biomedical Research, Adesh University, Bathinda, India. 2 Department of Clinical Biochemistry, Govt. College for Women, M. A. Road, Srinagar, Cluster University Srinagar, Kashmir, India. Item in Clipboard Saba Shabir et al. J Obstet Gynaecol Res. 2023. Show details…

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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets | BMC Bioinformatics

EasyCGTree was implemented in Perl programming languages (www.perl.org/) and was built using a collection of published reputable tools, including Clustal Omega version 1.2.4 [12]; consense from PHYLIP version 3.698 [13]; FastTree version 2.1 [14]; hmmbuild and hmmsearch from HMMER version 3.0 (hmmer.org/); IQ-TREE version 2.1.1 [15]; trimAl version 1.2 [16];…

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How to annotate function of genes from non-model organism

How to annotate function of genes from non-model organism 1 I conducted RNA differential expression analysis for a non-model organism and obtained a list of significantly different genes identified by their NCBI RefSeq IDs. However, I encountered difficulties in annotating the gene functions due to the limited availability of gene…

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BBTools 39.03 released!

Hi Everyone, I just released a new version of BBTools (39.03). There are some exciting new features like neural networks. But let me list them: 1) New program called “bbcrisprfinder.sh”. It finds CRISPRs… designed for short reads in metagenomes (but it’s also OK on full genomes). It works better if…

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Which alignment for whole bacterial genomes for phylogenetic tree?

Which alignment for whole bacterial genomes for phylogenetic tree? 0 I am supposed to build a phylogenetic tree out of around 200 bacterial genomes. They are not closely related. The first step is as far as I know alignment. My first plan was to do multiple sequence alignment with the…

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Aspiring Bioinformatics Analyst from Canada: Seeking Career Insights

Introduction & Education: Hey everyone, I’m Alex! I’ve recently earned my B.Sc. in Biochemistry & Molecular Biology from Canada. Bioinformatics has become my passion, and I aim to carve a career in the industry. In this post, I’m reaching out for guidance on the most suitable path forward. One key…

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DNA damage induced by CDK4 and CDK6 blockade triggers anti-tumor immune responses through cGAS-STING pathway

Patients’ tumor tissues and clinical data This study recruited 125 breast cancer patients for immunohistochemical (IHC) analysis and 10 breast cancer patients for RNA-seq analysis from the Affiliated Tumor Hospital of Nantong University. Tumor tissues collected from surgical patients were fixed with formalin and embedded with paraffin and then examined….

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python – How to BLAST a protein against a large set of organisms?

In the interface of blastp, you can limit the search space to organisms you want to. Yo can do this by introducing name species or Tax IDs, you can add more than one, but I bet you don’t wanna introduce the 1,500 one by one. The only other way to…

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BBTools 39.03 releaed!

Hi Everyone, I just released a new version of BBTools (39.03). There are some exciting new features like neural networks. But let me list them: 1) New program called “bbcrisprfinder.sh”. It finds CRISPRs… designed for short reads in metagenomes (but it’s also OK on full genomes). It works better if…

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BioPython BLAST unusable?

BioPython BLAST unusable? 0 I have been using BioPython to perform BLAST queries through NCBI. However, the speed is so slow, it is essentially unusable. The request below takes ~ 7 minutes to complete, while it only takes 11s to BLAST the same sequence using the webtool. I used the…

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Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells | Parasites & Vectors

Cell lines Hsu and CT cells originally derived from Culex quinquefasciatus and Culex tarsalis, respectively, were used as experimental material (gifts from R. van Rij, Radboud University, Nijmegen, the Netherlands). These cell lines are known to harbor several MSV infections [7]. Aag2 and C6/36 cells were received from A. Kohl…

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Edit fasta header for TSA submission

Edit fasta header for TSA submission 0 Hi everyone, I’ve been trying to edit the headers of my fasta file which is intend to upload on NCBI TSA. Can’t seem to successfully upload my file on TSA and if im not mistaken it could be because of the header format….

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Download NCBI data using sratool in anaconda

Download NCBI data using sratool in anaconda 0 Hello. I would like to download data from the PRJNA834801 project for analysis practice. I succeeded in installing sratoolkit in anaconda. How do I download all the data (725 data sets in the BioProject) of the project I want to download at…

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What is the new Entrez login for NCBI API?

What is the new Entrez login for NCBI API? 0 NCBI recently offloaded logging in to other websites. How do we reliably set the email and API key variables to use Entrez with the API key? I have attempted my legacy NCBI login and it appears to timeout after too…

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You are planning to study the activity of a protein

You are planning to study the activity of a protein which participates in proliferation of Vacciniavirus. You need to clone the relevant DNA in E. coli cell line. The gene of interest of your projectis 1711 bp long, linear and the details can be found in NCBI GenBank (accession number…

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Access to fastq files on SRA Run browser

Access to fastq files on SRA Run browser 0 Hi, as I was looking for sources to access fastq files directly instead of converting them from .sra and avoid the use of the SRA toolkit, I came across these links on the run browser which have aws s3 bucks links…

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To genetically characterize Fasciola adult worms

Introduction Fascioliasis is a zoonotic disease of public health significance and a worldwide distribution.1 The causative agents of Fascioliasis are F. hepatica (F. hepatica; temperate liver fluke) and Fasciola gigantica (tropical liver fluke).2,3 Although it has been recognized for centuries, the disease is currently expanding and has a serious impact…

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A new method for the detection of Mycobacterium tuberculosis based on the CRISPR/Cas system | BMC Infectious Diseases

Expression and purification of Cas12a protein The pMBP-LbCas12a recombinant plasmid used in this study was purchased from Addgene Global Plasmid Information Sharing Platform (Plasmid#113,431) and was 9653 bp in size. The recombinant plasmid was transformed into DH5α competent state and cultured at 37℃ for 6 h. IPTG was added at a final…

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Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article  PubMed  Google Scholar  Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article  ADS  CAS  PubMed …

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KEGG T00007: b1676

Entry b1676             CDS       T00007                                  Symbol pykF Name (RefSeq) pyruvate kinase I   KO K00873   pyruvate kinase [EC:2.7.1.40] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00010   Glycolysis / Gluconeogenesis eco00620   Pyruvate metabolism eco01100   Metabolic pathways eco01110   Biosynthesis of secondary metabolites eco01120   Microbial metabolism in diverse environments eco01200   Carbon metabolism eco01230   Biosynthesis of amino acids Module…

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Bioconductor BulkRNAseq

Comment: deseq2 filter the low counts by Michael Love 40k You can’t filter the groups separately, you need to use a non-specific filter that doesn’t make use of information about which samples are … Comment: deseq2 filter the low counts by daiane.hemerichbrennan • 0 Hi Michael, I have another question…

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Query regarding genome coverage in de-novo assembly

Query regarding genome coverage in de-novo assembly 1 we did some genome sequencing of bacteria from a biotech company, They used de-novo assembly for sequencing with Shovill assembly method using Illumina NovaSeq I need to submission those genome data in NCBI but the problem I am facing with their provided…

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Distribution tendencies of pathogens causing LRTI

Introduction Lower respiratory tract infection (LRTI) remains one of the leading causes of death worldwide.1 Several well-known pathogens, including Streptococcus pneumoniae, Pseudomonas aeruginosa, Klebsiella pneumoniae, Candida, Herpesvirus, and others, have been identified as significant causes of infection.2 Nonetheless, nearly half of the cases still have an undetermined etiology,3,4 despite the…

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Targeted knockout of a conserved plant mitochondrial gene by genome editing

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…

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Mutation in Polycomb repressive complex 2 gene OsFIE2 promotes asexual embryo formation in rice

CRISPR/Cas9-induced mutants at OsFIE1 and OsFIE2 Among ~150 T0 plants transformed with the CRISPR/Cas9 vector targeting the two FIE genes (Fig. 1a), we focused on plants with normal pollen dehiscence, as heterozygous fie mutants and other Polycomb mutants are not expected to give pollen sterility in heterozygous condition7,8,9,10,11,12,13,14. Four plants…

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Unraveling the secrets of the prevalent Staphylococcus strain

In a recent study published in Microbial Genomics, researchers investigated the genomes of a group of Staphylococcus capitis isolates from neonates. Study: Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults. Image Credit: Dmitry Kalinovsky/Shutterstock.com Background NRCS-A, a clone of S. capitis,…

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Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…

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A comprehensive dataset of animal-associated sarbecoviruses

Lytras, S., Xia, W., Hughes, J., Jiang, X. W. & Robertson, D. L. The animal origin of SARS-CoV-2. Science 373, 968–970 (2021). Article  ADS  CAS  PubMed  Google Scholar  Ye, Z. W. et al. Zoonotic origins of human coronaviruses. Int J Biol Sci 16, 1686–1697 (2020). Article  CAS  PubMed  PubMed Central …

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Actalent hiring 100% Remote- Bioinformatics Scientist in North Chicago, Illinois, United States

Seeking 1 Bioinformatics Scientist100% RemoteDescriptionWe are seeking a highly skilled and motivated contractor to join the Genomics Research Center and provide support for bioinformatics projects in the field of Ophthalmology and Specialty Medicine. As a contractor, you will collaborate with a team of scientists and researchers to analyze and interpret…

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Phylogenomics reveals the history of host use in mosquitoes

Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…

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MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

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Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype | Parasites & Vectors

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…

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How to BLAST a FASTA sequence with unknown organism source

How to BLAST a FASTA sequence with unknown organism source 0 I have a FASTA file including seven following contigs that I cannot find the origin of these contigs. >chrZ_001422_local >chrZ_012849_local >chrZ_012851_local >chrZ_012855_local >chrZ_012856_local >chrZ_012857_local >chrZ_014931_local I tried many BLAST tools such as ENSEMBLE, and NCBI and I could not…

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Solved Using the NCBI website, find the exact nucleotide

Using the NCBI website, find the exact nucleotide position of the folE gene start and stop in E. coli K-12 MG1655. Hint: make sure to search the “gene” database Is the gene on the + or – strand ? Find the names of the genes located before and after the…

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Virulence Characteristics of Salmonella Enteritidis

Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…

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Solved 1) Carry out a BLASTX search of the sequence below

1) Carry out a BLASTX search of the sequence below NCBI BLASTXsearching the non-redundant protein (nr) sequences database and using the invertebrate mitochondrial genetic code. Answer these 3 questions. 1) What protein does this sequence code for? 2) Which is the correct reading frame? 3) Which organism is the closest…

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[Solved] NCBI blast database – Biochemistry (Bsc221)

The NCBI Blast Database is a collection of sequence databases that can be used with the BLAST (Basic Local Alignment Search Tool) program. BLAST is a widely used bioinformatics tool for comparing nucleotide or protein sequences against a database to identify similarities and infer functional or evolutionary relationships. The NCBI…

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KEGG T01028: 717963

Entry 717963            CDS       T01028                                  Symbol STIM1 Name (RefSeq) stromal interaction molecule 1 precursor   KO K16059   stromal interaction molecule 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04020   Calcium signaling pathway mcc04611   Platelet activation Brite KEGG Orthology (KO) [BR:mcc00001] 09130 Environmental Information Processing  09132 Signal transduction   04020 Calcium signaling pathway    717963 (STIM1) 09150 Organismal Systems  09151 Immune system   04611 Platelet activation    717963…

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Progress and challenges in completing the human gene catalogue

In a recent review published in Nature, a group of authors reviewed the progress and challenges in annotating the human genome, including protein-coding genes, isoforms, and non-coding ribonucleic acids (RNAs), and advocated for a universal annotation standard for clinical use. Study: The status of the human gene catalogue. Image Credit:…

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US Tech Solutions hiring Bioinformatics Scientist in United States

Title: Bioinformatics Scientist Job type: Contract Duration: 06+ Months Client’s Location: Remote Job Description: We are seeking a highly skilled and motivated contractor to join the Genomics Research Center and provide support for bioinformatics projects in the field of Ophthalmology and Specialty Medicine. As a contractor, you will collaborate with…

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The status of the human gene catalogue

Understanding our Genetic Inheritance: The US Human Genome Project, The First Five Years 1991-1995 (US Department of Health and Human Services, US Department of Energy, 1990). Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). Describes the first complete gap-free assembly and annotation of…

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Coming Soon to ClinVar! Somatic Variants & Changes to the XML – NCBI Insights

Do you rely on ClinVar XML files for your application or analytical pipeline? We are significantly updating ClinVar’s XML format to support the inclusion of new somatic variation data provided by submitters. In the coming months, you may need to make changes to your tool or pipeline code to continue…

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KEGG T05149: 103473078

Entry 103473078         CDS       T05149                                  Symbol ppt1 Name (RefSeq) palmitoyl-protein thioesterase 1 isoform X1   KO K01074   palmitoyl-protein thioesterase [EC:3.1.2.22] Organism pret  Poecilia reticulata (guppy) Pathway pret00062   Fatty acid elongation pret01100   Metabolic pathways pret01212   Fatty acid metabolism pret04142   Lysosome Brite KEGG Orthology (KO) [BR:pret00001] 09100 Metabolism  09103 Lipid metabolism   00062 Fatty acid elongation    103473078 (ppt1) 09140 Cellular Processes  09141 Transport and…

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KEGG T05897: 110480856

Entry 110480856         CDS       T05897                                  Symbol AGA Name (RefSeq) N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase   KO K01444   N4-(beta-N-acetylglucosaminyl)-L-asparaginase [EC:3.5.1.26] Organism lsr  Lonchura striata domestica (Bengalese finch) Pathway lsr00511   Other glycan degradation lsr04142   Lysosome Brite KEGG Orthology (KO) [BR:lsr00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00511 Other glycan degradation    110480856 (AGA) 09140 Cellular Processes  09141 Transport and catabolism   04142 Lysosome    110480856 (AGA)Enzymes [BR:lsr01000] 3. Hydrolases  3.5  Acting on carbon-nitrogen bonds,…

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KEGG T02867: BN877_I0744

Entry BN877_I0744       CDS       T02867                                  Symbol coxB1 Name (GenBank) cytochrome c oxidase, subunit II   KO K02275   cytochrome c oxidase subunit II [EC:7.1.1.9] Organism rir  Agrobacterium pusense IRBG74 Pathway rir00190   Oxidative phosphorylation rir01100   Metabolic pathways Module rir_M00155   Cytochrome c oxidase, prokaryotes Brite KEGG Orthology (KO) [BR:rir00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BN877_I0744 (coxB1)Enzymes [BR:rir01000] 7. Translocases  7.1  Catalysing the…

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OmniAb, Inc. hiring Senior Bioinformatics Scientist in Emeryville, California, United States

We are seeking a Senior Bioinformatics Scientist to support our ongoing antibody discovery and genetic engineering efforts. The role includes refining custom tools and algorithms to facilitate identification of therapeutic leads from OmniAb immune repertoires and applying cutting edge computational biology approaches to all stages of antibody discovery, from antigen…

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University of Washington hiring BIOINFORMATICS ENGINEER in Seattle, Washington, United States

Req #: 226825 Department: LABORATORY MEDICINE AND PATHOLOGY Posting Date: 10/02/2023 Closing Info: Open Until Filled Salary: $6843 – $11120 per month Shift: First Shift Notes: As an employee you will enjoy generous benefits and work/life programs. For detailed information on Benefits for this position, click here. ( hr.uw.edu/benefits/wp-content/uploads/sites/3/2018/02/benefits-professional-staff-librarians-academic-staff-20230119_a11y.pdf) The…

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RefSeq: XP_024590519

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;…

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KEGG T08832: 125909104

Entry 125925080         CDS       T08832                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2 isoform X1   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism puc  Panthera uncia (snow leopard) Pathway puc00230   Purine metabolism puc00250   Alanine, aspartate and glutamate metabolism puc01100   Metabolic pathways puc01232   Nucleotide metabolism puc01240   Biosynthesis of cofactors Module puc_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG…

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Bioconductor – SNPlocs.Hsapiens.dbSNP142.GRCh37

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP142.GRCh37     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP142.GRCh37. SNP locations for Homo sapiens (dbSNP Build 142) Bioconductor version: 3.13 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for…

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Transforming Healthcare With Generative AI

Generative AI is selling itself to emerge as the new frontier in the horizon for the booming healthcare industry. Highlighting some of the significant developments in this technology space, this article has a few Indian leaders voicing their opinions on exploring Generative AI to progress their businesses and services. Generative…

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RNAseq based variant dataset in a black poplar association panel | BMC Research Notes

Dickmann DI, Kuzovkina J. Poplars and willows of the world, with emphasis on silviculturally important species. In: Isebrands JG, Richardson J, editors. Poplars and willows: trees for society and the environment. Wallingford: CABI; 2014. Google Scholar  Imbert E, Lefèvre F. Dispersal and gene flow of Populus nigra (Salicaceae) along a…

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KEGG T00061: RC0581

Entry RC0582            CDS       T00061                                  Symbol pheT Name (GenBank) phenylalanyl-tRNA synthetase beta chain   KO K01890   phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20] Organism rco  Rickettsia conorii Pathway rco00970   Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:rco00001] 09120 Genetic Information Processing  09122 Translation   00970 Aminoacyl-tRNA biosynthesis    RC0582 (pheT) 09180 Brite Hierarchies  09181 Protein families: metabolism   01007 Amino acid related enzymes [BR:rco01007]    RC0582 (pheT)  09182 Protein families: genetic…

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Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease | Orphanet Journal of Rare Diseases

Macken WL, Vandrovcova J, Hanna MG, Pitceathly RDS. Applying genomic and transcriptomic advances to mitochondrial medicine. Nat Rev Neurol. 2021;17(4):215–30. doi.org/10.1038/s41582-021-00455-2 Article  PubMed  Google Scholar  Gorman GS, Chinnery PF, DiMauro S, Hirano M, Koga Y, McFarland R, et al. Mitochondrial diseases. Nat Rev Dis Primers. 2016;2(1). doi.org/10.1038/nrdp.2016.80 Barcia G, Assouline…

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The Clinical Impact of mNGS for the Diagnosis of PJI

Introduction The total number of periprosthetic joint infection cases is increasing with the surging numbers of joint arthroplasties, internal fixation implantation and the use of immunosuppressive agents.1,2 Unfortunately, the identification of corresponding pathogens remains time-consuming and challenging because of inert bacteria, biofilm formation and prior antibiotic administration.3–8 Metagenomic next-generation sequencing…

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Challenges and opportunities in sharing microbiome data and analyses

Kyrpides, N. C., Eloe-Fadrosh, E. A. & Ivanova, N. N. Microbiome data science: understanding our microbial planet. Trends Microbiol. 24, 425–427 (2016). Article  CAS  PubMed  Google Scholar  Winkler, T. W. et al. Quality control and conduct of genome-wide association meta-analyses. Nat. Protoc. 9, 1192–1212 (2014). Article  PubMed  PubMed Central  Google…

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RefSeq: XP_033346483

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;…

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How to install ncbi-rrna-data on Ubuntu

Install ncbi-rrna-data Installing ncbi-rrna-data package on Ubuntu is as easy as running the following command on terminal: sudo apt-get update sudo apt-get install ncbi-rrna-data ncbi-rrna-data package information More information about install using apt-get Advanced Package Tool, or APT, is a free software user interface that works with core libraries to…

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Whole transcriptome analysis in offspring whose fathers were exposed to a developmental insult: a novel avian model

Werboff, J. & Gottlier, J. S. Drug in pregnancy: Behavioral teratology. Obstet. Gynecol. Surv. 18, 420–423 (1963). Article  Google Scholar  Yanai, J. G. The effect of alcohol consumed by parent mice on the susceptibility to audiogenic seizure and the open-field behavior of their offspring. Behav. Genet. 3, 418 (1973). Google…

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Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Chloroplast genome features of four Polygonatum species In this phase of our study, we pursued the sequencing of four Polygonatum species namely P. filipes, P. cyrtonema, P. zanlanscianense and P. odoratum, using the Illumina HiSeq 2500 sequencing platform. This endeavour yielded a corpus of Illumina reads ranging from 15,915,998 to…

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Purpose, Types, Applications, Bioinformatics and more

Next-Generation Sequencing (NGS), also known as high-throughput sequencing, is a revolutionary technology used for determining the sequence of DNA or RNA molecules. It has significantly advanced the field of genomics and has numerous applications in various biological and medical fields. Key Points of Next-Generation Sequencing (NGS): Revolutionary Technology: NGS represents…

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KEGG T00123: EF1761

Entry EF1761            CDS       T00123                                  Symbol ftsE Name (RefSeq) cell division ATP-binding protein FtsE   KO K09812   cell division transport system ATP-binding protein Organism efa  Enterococcus faecalis V583 Pathway efa02010   ABC transporters Brite KEGG Orthology (KO) [BR:efa00001] 09130 Environmental Information Processing  09131 Membrane transport   02010 ABC transporters    EF1761 (ftsE) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03036 Chromosome and associated…

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The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…

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A tool to automatically design multiplex PCR primer pairs for specific targets using diverse templates

PMPrimer software PMPrimer is a Python-based tool for the automated design and evaluation of multiplex PCR primer pairs for specific targets using diverse templates (Fig. 1). To satisfy the need for automation, PMPrimer can directly extract taxonomic information at three levels of classification (genus, species, and subspecies) from input data in…

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KEGG T00835: Ccel_0126

Entry Ccel_0126         CDS       T00835                                  Name (GenBank) 3-isopropylmalate dehydratase, large subunit   KO K01703   3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35] Organism cce  Ruminiclostridium cellulolyticum Pathway cce00290   Valine, leucine and isoleucine biosynthesis cce00660   C5-Branched dibasic acid metabolism cce01100   Metabolic pathways cce01110   Biosynthesis of secondary metabolites cce01210   2-Oxocarboxylic acid metabolism cce01230   Biosynthesis of amino acids Module cce_M00432  …

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DETECTING GENETIC ENGINEERING WITH A KNOWLEDGE-RICH DNA SEQUENCE CLASSIFIER

Abstract Detecting evidence of genetic engineering in the wild is a problem of growing importance for biosecurity, provenance, and intellectual property rights. This thesis describes a computational system designed to detect engineering from DNA sequencing of biological samples and presents its performance on fully blinded test data. The pipeline builds…

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Solved You published a paper on complete genomes of the

Transcribed image text: You published a paper on complete genomes of the mitochondrion of Caenogastropoda (mostly marine snails) late in 2016. You decide to check on GenBank to see how many complete genomes for the mitochondrion of Caenogastropoda have been published from the beginning of 2017 to present. Construct and…

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BLAST WASM

BLAST is a family of tools used to compare biological sequences, such as protein or DNA sequences, against a database of sequences. It is used in bioinformatics applications, including genome annotation, gene discovery, and phylogenetic analysis of DNA and protein sequences. The BLAST source code is written in C++ and…

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