Tag: GenBank

can i skip cutadapt?? – User Support

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…

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Summary of Escherichia coli K-12 substr. MG1655, version 26.0

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

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Identification of the genetic elements involved in biofilm formation by Salmonella enterica serovar Tennessee using mini-Tn10 mutagenesis and DNA sequencing

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…

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How to identify locus_tag by using RefSeq protein info (WP_*)

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

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First genomic sequencing of monkeypox from Switzerland is now available

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…

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Create a streamlit download_button to download a fasta file from a local Genbank file – Using Streamlit

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…

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Splitting a GenBank file into smaller files

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

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

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…

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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/incr_time.cpp Source File

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

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Get reference genome from Kraken2 taxID

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…

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LOC125105370 sterile alpha motif domain-containing protein 1-like [Lutra lutra (Eurasian river otter)] – Gene

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…

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Parsing GenBank file: get locus tag vs product

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”…

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socket.gaierror while downloading genbank files w/ biopython

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

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Append assembly accession to nucleotide accession number in RefSeq Genbank file

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…

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How to get the scientific name given the GenBank accession code to biopython?

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’)…

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

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

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What is ClustalW? Tutorial of How to Use ClustalW

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…

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

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

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Extensively drug resistant E. coli LZ00114

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

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Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

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…

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Extracting exact location of interest from genbank file

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…

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how to downolad genbank file from islandviewer

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…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

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…

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

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

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The meaning of greter than character (>) in gene position in Genbank files

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…

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

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

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

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

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Hinted by Clinical Misclassification of a Neisseria mucosa Strain

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,…

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

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

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

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

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KEGG T03334: R50912_07385

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

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(PDF) GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database | Flavio Licciulli

(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…

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dbSNP – Wikipedia @ WordDisk

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

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Amur ide genome – assembly database

 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…

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WikiHr > 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),…

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Petabase-scale sequence alignment catalyses viral discovery

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…

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man subfuse (1): merge Genbank submissions

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…

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Phihlikevirus

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…

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Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

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…

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genbank – Github Help

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…

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Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

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”….

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Human Mitochondrial Genome Feature Table for GenBank BankIt

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….

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genbank to GTF in galaxy

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…

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Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

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…

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Question : Improve genbank feature addition

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…

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Dryad Data — Lichen fungi do not depend on the alga for ATP production

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…

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some signatures that have been suppressed by RefSeq/GenBank are not in wort

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…

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A pandemic-scale phylogenetic analysis tool

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,…

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Study finds sarbecoviruses circulating in wildlife outside Asia can infect human cells

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…

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Load .gb file in R

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’…

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PhD Bioinformatics, Computer Science, Data Science – Imformatics & Policy, Bibliometrics (m/f/d), Braunschweig – Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH – Computer Sciences

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…

Continue Reading PhD Bioinformatics, Computer Science, Data Science – Imformatics & Policy, Bibliometrics (m/f/d), Braunschweig – Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH – Computer Sciences

Transcriptome assembly, annotation and submission to GenBank for unannotated organisms

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…

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How To Download .Gbk Files From Ncbi Website

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…

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Submit sequence data to NCBI

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

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Biopython Contact Map | Contact Information Finder

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….

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PolyAllele Detail

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…

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GenBank Biologist – Bethesda, MD

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…

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Genomic features of a carbapenem-resistant K. oxytoca strain

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,…

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Phylogeographic reconstruction of the marbled crayfish origin

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…

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Liftover nonmodel VCF

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…

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Mutational Analysis of Mitochondrial tRNA Genes

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,…

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Cosmo_00080 : CDS information — DoBISCUIT

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

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Pact_00210 : CDS information — DoBISCUIT

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

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

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

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Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

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…

Continue Reading Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

Genomic and phenotypic characteristics for Vibrio vulnificus

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…

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

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…

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Bacterial morphology details

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)….

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UCSC knownCanonical hg19 vs. hg38

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…

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Is there way to get genbank assembly id from nuccore id using ncbi eutils ?

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…

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Koala retrovirus genetic diversity and transmission dynamics within captive koala populations

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…

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Stref_00240 : CDS information — DoBISCUIT

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

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an app for Mac users to convert .xdna and .dna files into genbank .gb files and more

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…

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Download intergenic spacers between specific genes for all findings in genbank

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…

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DNA Barcode as an effective tool in the identification of billfishes (Scombroidei, Teleostei) from exported specimens

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…

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parsing gbk files (antismash result)

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”):…

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Insects | Free Full-Text | MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity

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…

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Emergence of the Coexistence of mcr-1, blaNDM-5, and blaCTX-M-55 in Kl

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…

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New frog on the block!

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….

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Aspartyl protease from Trichoderma harzianum CECT 2413: cloning and characterization The GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AJ276388.

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…

Continue Reading Aspartyl protease from Trichoderma harzianum CECT 2413: cloning and characterization The GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AJ276388.

best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi)

best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi) 1 What would be the best way (if there is any) to get the accession number of a genome assembly that contains a given protein accession number? E.g. if i just have the results of a blastp…

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How to access NCBI .bbs files

How to access NCBI .bbs files 0 Hello, I’m trying to find genome annotation information for a genome that has been uploaded to NCBI. The only downloadable files that I can find for this genome are the Genbank file (.gbff), FASTA file (.fsa_nt), and something called ASN.1 (.bbs). Knowing that…

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Haplogroup H1e1a

Phylogenetic tree of complete haplogroup H1e1a sequences. Y-DNA Haplogroup R-M207 Summary Haplogroup R is defined by a DNA marker known as M207. Significant frequencies of sub-Saharan L haplogroups (6. Haplogroup H is a human mitochondrial DNA (mtDNA) haplogroup. The report also said 0. Just out of curiosity, I noticed that…

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Taking the Pulse of the Ocean’s Comb Jellies

The enormousness of the global sea has, over ages of exploration, made the appraisals of prime inhabitants more like rough sketches than detailed portraits. Now, scientists have devised a precise way of detecting one of the ocean’s more exotic creatures. Estimates of its global abundance, they say, will likely soar….

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Biostar Genbankr

Showing : genbankr • reset updated 8 months ago by Nicholas • 0 • written 8 months ago by heiko_kin &utrif; 50 9 results • Page 1 of 1 Traffic: 479 users visited in the last hour Read more here: Source link

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Ribon Therapeutics hiring Principal Scientist Bioinformatics in Cambridge, MA, US

About Ribon Therapeutics Ribon is a clinical-stage biotechnology company dedicated to the discovery and development of first-in-class small molecule inhibitors to block the fundamental ability of cancer cells to survive under stress. Job Description Ribon Therapeutics, a clinical biopharmaceutical company focused on targeting stress pathways to develop novel cancer therapeutics,…

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Prevalence and Molecular Characteristics Based on Whole Genome Sequenc

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…

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Helicobacter pylori in Pakistan | IDR

Introduction Helicobacter pylori, an infectious agent of human chronic active gastritis and also associated with other gastric ailments such as peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue lymphoma.1 Clarithromycin is considered the best option among other antibiotics for the management of this bacterial infection.2 However, increasing resistance against this…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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Download Assembled Genomes NOT in RefSeq

Download Assembled Genomes NOT in RefSeq 0 I have a list of NCBI accession numbers and I need to download the genome sequence (or assemblies) in FASTA format. I can accomplish this for genomes that are present in RefSeq using the following command: esearch -db nuccore -query GCF_900343155.1 | efetch…

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New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

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SRA splitting for each metagenome-assembled genome

Job:SRA splitting for each metagenome-assembled genome 0 Hi everybody, we obtained viruses from water and sequenced them with Illumina. we formed different metagenomic-assembled genomes and get a Bioproject number and Biosample numbers (for each of them). Now, i should do SRA submission. But i cannot submit for my all genomes…

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STAR rna-seq for bacterial genomes

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

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