Tag: GenBank

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …

How to retrieve all genes of interest from GenBank? 1 Hello Bioinformagicians! My goal is to create a phylogenetic tree using mitochondria genes of ticks. I’ve recently use genes taken from Refseq complete genomes. However, I want to include gene sequences that may not be part of complete genomes. How…

Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…

Overview of the viromes In all, 41 wild Qinghai voles were collected from pasture habitats located on the eastern Tibetan Plateau, China (Fig. 1). Tissue samples from liver, lung, spleen, small intestine (with content), and feces (large intestinal content) of each vole were disrupted, and viral RNA was extracted. The RNA…

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

Number of sequences in RefSeq. 2 Dear colleagues I can not understand. When I download all the genomic sequences from the refseq database, after counting, I see that there are much fewer records than presented in the release (123394 organisms ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release214.txt). What am I doing wrong? 1. wget ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt 2….

KoRV genetic diversity Illumina env amplicon deep sequencing was carried out on genomic DNA isolated from the peripheral blood mononuclear cells (PBMCs) of 64 koalas housed in three captive koala colonies within Australia, one in South-East Queensland (SE QLD; colony C, n = 33) and two in Sydney, New South Wales (NSW;…

RefSeq release 214 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in…

So I am trying to parse through a gene bank file, extract particular feature information and output that information to a csv file. The example gene bank file looks like this: SBxxxxxx.LargeContigs.gbk LOCUS scaffold_31 38809 bp DNA UNK 01-JAN-1980 DEFINITION scaffold_31. ACCESSION scaffold_31 VERSION scaffold_31 KEYWORDS . SOURCE . ORGANISM…

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

Animal and ethics A total of 190 dogs, comprising both healthy dogs (n = 76) and dogs with respiratory symptoms (n = 114), were included in this study. The research assessed nasal swab (NS) and oropharyngeal swab (OS) collected between January and November 2020. The samples from the healthy group were collected from clinically…

The isolate is a qualifier of the source feature that you can access like so: from Bio import SeqIO from pprint import pprint # Read genbank file for rec in SeqIO.parse(“genome.gb”, “genbank”): source = rec.features[0] pprint(source.qualifiers) will print: OrderedDict([(‘organism’, [‘Amauroderma calcitum’]), (‘mol_type’, [‘genomic DNA’]), (‘isolate’, [‘FLOR 50931’]), (‘db_xref’, [‘taxon:1774182’]), (‘country’,…

Implementation of a high-resolution barcoding system In order to determine the clonal relationships of developing thymocytes, we used an endogenous barcoding system (Fig. 1a) that consists of three components19. (i) A construct for the ubiquitous expression of the Hprt gene-specific sgRNA (hU6:sgRNAHprt)19; (ii) A conditional Cas9 expression construct (Rosa26:LSL-Cas9-YFP) inserted into…

Login page for ncbi wgs portal is presented below. Log into ncbi wgs portal page with one-click or find related helpful links. Last Updated: 17th August, 2022 WGS – NCBI – NIH   www.ncbi.nlm.nih.gov/genbank/wgs Nov 13, 2017 – Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or…

Developing countries feel digital sequence information provides a loophole through which developed countries can circumvent the Convention of Biodiversity Negotiations on how to regulate the use of digital sequence information (DSI) of genetic resources could further delay the finalisation of the Post-2020 Global Biodiversity Framework under the UN Convention on Biological Diversity (CBD)….

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution…

GenBank (Q25257250) scientific article (published 2006-01-01) Language: Englishfrançais (French)español (Spanish)Deutsch (German)dansk (Danish)Nederlands (Dutch)汉语 (Chinese)العربية (Arabic)italiano (Italian)latviešu valoda (Latvian)eesti keel (Estonian)suomi (Finnish)português (Portuguese)svenska (Swedish)Norsk (Norwegian)日本語 (Japanese)हिन्दी (Hindi)Lëtzebuergesch (Luxembourgish) Read more here: Source link

Hey guys, I’ve written this python code. import pandas as pd from Bio import SeqIO import argparse parser= argparse.ArgumentParser(add_help=False) parser.add_argument(“-h”, “–help”, action=”help”, default=argparse.SUPPRESS, help= “Get partial gff given a pattern on Names field”) parser.add_argument(“-g”, help= “-g: gff file”, required = “True”) parser.add_argument(“-l”, help= “-l: list of patterns to search on…

Candolleomyces asiaticus sp. nov. (Psathyrellaceae, Agaricales), a novel species from Punjab, Pakistan Author Asif, Muhammad Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan. asifgondal101@gmail.com Author Izhar, Aiman Fungal Biology and Systematics Research Laboratory, Institute of Botany, University of the Punjab,…

recently i receive rowdata from NGS center..and i start analysis using QIIME2 i want ‘cutadapt’, so i ask primer sequence to NGS center..but center reply to me “it is secret” if it is neccessery, i request to NGS center…. thank u for reading Hi @svbreqwaiu01, You do not need to…

Summary of Escherichia coli, Strain K-12 substr. MG1655, version 26.0 Tier 1 Highly Curated Database Authors: Peter D. Karp1, Ingrid Keseler1, Carol Fulcher1, Anamika Kothari1, Suzanne Paley1, Markus Krummenacker1, Ian Paulsen2, Amanda Mackie2, Julio Collado-Vides3, Cesar Bonavides-Martinez3, Socorro Gama-Castro3, Alberto Santos-Zavaleta3, Victor H Tierrafria3 1SRI International, 2Macquarie University, 3Centro de…

doi: 10.1016/j.fm.2022.104043. Epub 2022 Apr 23. Affiliations Expand Affiliations 1 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. 2 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. Electronic address: jchen@uga.edu. Item in…

How to identify locus_tag by using RefSeq protein info (WP_*) 0 Hi, I would like to know the locus tag of a protein annotated with RefSeq (WP_*). For example, I would like to identify the genomic location of a protein (WP_073031595.1) and also know its adjacent proteins. The GenBank file…

The virus can be identified with a PCR test, especially from affected lesions and other samples. Credit: Geneva University Hospitals (HUG) The Geneva Centre for Emerging Viral Diseases shares the first sequencing results of the monkeypox genome from Switzerland. This important step will enable further analysis and comparison with genome…

Hi streamlit communityI’m building a streamlit app that allows the users to upload a full record genbank file and to explore its content (genes sequences, proteins sequences etc.) using biopython. Everything works perfectly except when I try to create a st.download_button() to download the hole genome sequence or a sequence…

19  Upvotes · 1 Comments 18  Upvotes · 1 Comments 20  Upvotes · 1 Comments 24  Upvotes · 1 Comments 19  Upvotes · 1 Comments 24  Upvotes · 1 Comments 24  Upvotes · 1 Comments Read more here: Source link

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

Go to the documentation of this file. Go to the SVN repository for this file. 44  const string& driver_name, 47  m_InitTime = x_GetDoubleParam(conf, driver_name, params.m_Initial); 48  m_MaxTime = x_GetDoubleParam(conf, driver_name, params.m_Maximal); 49  m_Multiplier = x_GetDoubleParam(conf, driver_name, params.m_Multiplier); 50  m_Increment = x_GetDoubleParam(conf, driver_name, params.m_Increment); 55  const string& driver_name, 68  if (…

Get reference genome from Kraken2 taxID 0 I have a ~10Gb ONT metagenome from citrus psyllid that I am trying to extract bacterial contigs from to assemble. My current thought for a pipeline is broadly as follows: Tentative ID of each contig with Kraken2, then QC to only take assignments…

The following sections contain reference sequences that belong to a specific genome build. Explain This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. Model RNAs and proteins are also…

As your sample GenBank file was incomplete, I went online to find a sample file that could be used in an example, and I found this file. Using this code and the Bio::GenBankParser module, it was parsed guessing what parts of the structure you were after. In this case, “features”…

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

Append assembly accession to nucleotide accession number in RefSeq Genbank file 0 Hi everyone, When I want to append the filename to the contig header in a multi-fasta file, I usually use for F in *.fasta; do N=$(basename $F .fasta) ; bbrename.sh in=$F out=${N}_mod.fasta prefix=$F addprefix=t ; done However, this…

Note that output is a dictionary. You can access any appropriate fields if needed. Also, you would want to use efetch, as opposed to esearch. In [1]: from Bio import Entrez In [3]: Entrez.email = ‘##############’ In [28]: handle = Entrez.efetch(db=”nucleotide”, id=”AY851612″, rettype=”gb”, retmode=”text”) In [29]: x = SeqIO.read(handle, ‘genbank’)…

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

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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

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

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

Extracting exact location of interest from genbank file 3 Hi everyone, I am trying to find any infromation how to extract the known cordinates from the genbank file but had no luck so far. This is how i have my results where the top line is the chromosome and from…

how to downolad genbank file from islandviewer 0 Dear All, am working on a salmonella st313 genome which i uploaded on islandViewer to try and get genomic islands, i want to download a genbank file i can use to visualize the islands on artemis but i cant seem to find…

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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

The meaning of greter than character (>) in gene position in Genbank files 1 Hello.This character made some issues when I used Genbank files’ contents.Here an example of ‘>’ usage in a Genbabk file: gene 957467..>957886 /locus_tag=”BME_RS04610″ /old_locus_tag=”BMEI0926″ I couldn’t find what ‘>’ signifies. Does anyone knows? genbank • 120…

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

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

The taxonomy of the genus Neisseria remains confusing, particularly regarding Neisseria mucosa and Neisseria sicca. In 2012, ribosomal multi-locus sequence typing reclassified both as N. mucosa, but data concerning 17 N. sicca strains remain available in GenBank. The continuous progress of high-throughput sequencing has facilitated ready accessibility of whole-genome data,…

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

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

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

(PDF) GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database | Flavio Licciulli – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies…

The Single Nucleotide Polymorphism Database[1] (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of…

 Home Assembly GCA_900092035.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_900092035.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

Database containing reference sequences of genes, proteins and transcripts The Reference Sequence (RefSeq) database[1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was first introduced in 2000.[2][3] This database is built by National Center for Biotechnology Information (NCBI),…

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

subfuse(1) merge Genbank submissions SYNOPSIS subfuse [–] [-o filename] [-p path] [-x ext] DESCRIPTION subfuse is a utility to consolidate multiple Genbank submissions into a single batch submission. OPTIONS A summary of options is included below. – Print usage message -o filename Output file (stdout by default) -p path Path to files -x ext Input filename…

Phihlikevirus (synonym: PhiH-like viruses) is a genus of viruses in the order Caudovirales, in the family Myoviridae. Bacteria and archaea serve as natural hosts. There is currently only one species in this genus: the type species Halobacterium phage phiH.[1][2] Taxonomy Group: dsDNA [2] Structure Phihlikeviruses are nonenveloped, with a head…

Significance The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic…

7 1 4 genbank,MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from…

The detection of viruses As shown in Table 1, viral NGS identified at least one syndrome-associated mammalian virus in 35 of 95 Kilifi County Hospital (KCH) inpatient samples (36.8%) and 23 of 95 household cohort (study investigating Who-Acquires-Infection-From-Whom, WAIFW) samples (24.2%), leading to an overall 30.5% “missed virus detection rate”….

Human Mitochondrial Genome Feature Table for GenBank BankIt 0 Hello Bioinfo Stars, I would like to submit human mitochondrial genome sequences to GenBank using BankIt portal, but encountered problem with the preparation of the five column Feature Table. As you may know, Feature Table for mitochondrial genomes of Metazoa (i.e….

genbank to GTF in galaxy 0 Hi all, I am working on galaxy and have a genome file in genbank format. To use featurecounts for my RNAseq, I need to convert the genbank format to a GTF format because that’s the format the featurecounts tool in galaxy expects. Now, I…

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

Question Improve genbank feature addition * 60 visibility 0 arrow_circle_up 0 arrow_circle_down I am trying to add more than 70000 new features to a genbank file using biopython. I have this code: from Bio import SeqIO from Bio.SeqFeature import SeqFeature, FeatureLocation fi = “myoriginal.gbk” fo = “mynewfile.gbk” for result in…

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit…

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

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2) and past SARS-CoV outbreaks were a result of zoonotic spillover of sarbecoviruses from animals to humans. Although most of the animal sarbecoviruses do not infect eukaryotic cells, clade 4 sarbecoviruses recently found in China…

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

OPEN POSITION32/21 Informatics and policy post-doc (m/f/d) at the Leibniz-Institute DSMZ-German Collection Microorganisms and Cell Cultures GmbH In a new science policy project “Examining Trends in Non-Monetary Benefit-Sharing” (ET-NMBS) funded by the German Federal Agency for Nature Conservation (BfN), we will develop new methods to contribute to the UN Convention…

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

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

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…

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

Polymorphism: FLAG_344G02 Name    FLAG_344G02 Date last modified    2006-09-11 Aliases    344G02 Tair Accession    Polymorphism:1009991284 Type    insertion    Insertion Type    T-DNA Chromosome   unknown Mutagen    T-DNA insertion Mutation Site    gene Associated Polymorphisms Insertion   Species Variant (attribution)   Length   Polymorphic Sequence   Polymorphism…

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

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

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

Liftover nonmodel VCF 1 Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I’ve found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can…

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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…

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)….

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…

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars…

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

Bacterial morphology details 1 hi, I have a list of bacteria (~ >2000), is there a data source or a way (other than manual literature study) i can get information like- its shape (cocci, rod or spiral), whether it is gram positive or negative and respiration detail (Anaerobic or Aerobic)….

Hello, We have an FAQ page that covers this topic (genome.ucsc.edu/FAQ/FAQgenes.html#singledownload). As posted by ATpoint, it boils down to different datasets and different approaches. hg19 knownCanonical was last updated in 2013 and built primarily from RefSeq and GenBank sequences and a few other sources. One isoform was identified from each…

Is there way to get genbank assembly id from nuccore id using ncbi eutils ? 2 Hello, I am trying to get the assembly id (for eg. GCA_000312685.1 ) for the nuccore id (CP003157.1) using eutils? For the WGS nuccore id such as CAJY00000000 you can get the the assembly…

Significance A conserved retrovirus, koala retrovirus (KoRV)-A, is present within the genome of koalas in most Australian populations. Additional divergent sequences and subtypes are thought to be exogenously transmissible and more pathogenic. We present a comprehensive analysis of KoRV genetic diversity within two captive koala populations and statistically significant evidence…

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。 …

Tool:BioFileConverter – an app for Mac users to convert .xdna and .dna files into genbank .gb files and more 1 Here I would like to present a small app – BioFileConverter for Mac users. This app can be very useful for the conversion of a large number of .xdna (SerialCloner…

Download intergenic spacers between specific genes for all findings in genbank 0 Good afternoon, I want to download fasta from genbank for intergenic spacers between certain genes for a taxon (for example, atpB-rbcL from the chloroplast genome). If I were downloading fasta for a single gene (GENE), I would do…

Available online 28 August 2021, 100028 Abstract DNA Barcode were used to identify species Billfishes and swordfish Xiphias gladius appeared as the only billfish species exported in Brazil. This system has been used successfully in the identification of species and samples not characterized, or illegally traded, as well as products…

parsing gbk files (antismash result) 0 Hello I used antismash from the CLI and I got 700 gbk files (1 gbk file per each analyzed genome). I used the following script to retrieve the predicted products from the gbk files: from Bio import SeqIO import glob for files in glob.glob(“*.gbk”):…

Local populations of Apis mellifera are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial tRNAleu-cox2 intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine…

Introduction Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen and the leading cause of healthcare-associated infections.1 Multidrug-resistant (MDR) K. pneumoniae isolates are rapidly spreading, thus limiting the choice of antimicrobial agents for empiric treatment of infections caused by these microorganisms; hence, this is a public health challenge.2 Polymyxins are last-resort…

The worldwide scientific community is too often bombarded with bad news — from first time ever rains at the Greenland ice summit to the Intergovernmental Panel on Climate Change’s (IPCC) doomsday forecast, there is hardly ever a reason to celebrate. Yet for Bangladesh’s nature enthusiasts, there is cause to celebrate….

scite is a Brooklyn-based startup that helps researchers better discover and evaluate scientific articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by researchers from dozens of countries and is funded in part by the…