Tag: tRNA

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq 0 Hi all, I have some small RNA-seq libraries from some plants. I downloaded ncRNA from Ensemble Plants as I don’t know how to use the Rfam database. How could I extract the rRNA/tRNA and other ncRNA ratios…

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Root70 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/29/2015 14:17:23 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes::4,587 CDS::4,486 Pseudo Genes::46 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S, 23S) partial rRNAs:: tRNAs::51 ncRNA::1 ##Genome-Annotation-Data-END##…

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Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”

Since 2010, there have been multiple new species added to the Listeria genus, many originally isolated from natural environments16. This paper describes the genotypic and phenotypic characterization of two new Listeria isolates obtained from soil samples collected in the Great Smoky Mountains National Park along the North Carolina-Tennessee border17. Evaluation…

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Convenience-sized RNA editing | MIT News

Last year, researchers at MIT’s McGovern Institute for Brain Research discovered and characterized Cas7-11, the first CRISPR enzyme capable of making precise, guided cuts to strands of RNA without harming cells in the process. Now, working with collaborators at the University of Tokyo, the same team has revealed that Cas7-11…

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GENCODE – Human Release 32 Statistics

Statistics about the GENCODE Release 32 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 60609 Protein-coding genes 19965 Long non-coding RNA genes 17910…

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In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

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Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

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tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

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Solved 28) What structure below provides an “anticodon”?

Transcribed image text: 28) What structure below provides an “anticodon”? (2pts) OmicroRNA mRNA tRNA rRNA 29) Which of the following modifications is involved in the 3′ (three prime) end-processing of pre- (4pts) mRNA precursors in eukaryotic cells? Addition of a methlyguanosine cap Splicing out introns Addition of Poly-A tail Forming…

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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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PDT001259745.1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Date::03/08/2022 21:07:51 Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Provider::NCBI Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Annotation Software revision::2021-01-11.build5132 Genes (total)::5,850 CDSs (total)::5,754 Genes (coding)::5,653 CDSs (with protein)::5,653 Genes (RNA)::96 rRNAs::4, 2, 3 (5S, 16S, 23S) complete rRNAs::4 (5S) partial…

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CRISPR/Cas9 deletions induce adverse on-target genomic effects

Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) have transformed genome engineering techniques. Numerous toolsets have been created to enable easy and efficient loss-of-function perturbations of functional genomic sites. Study: CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells. Image Credit: elenabsl/Shutterstock The CRISPR/Cas9 system’s elements…

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Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

This article was originally published here Genes (Basel). 2022 Mar 28;13(4):601. doi: 10.3390/genes13040601. ABSTRACT Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have…

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ASM1860456v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/02/2021 10:26:31 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,541 CDSs (total)::3,440 Genes (coding)::3,416 CDSs (with protein)::3,416 Genes (RNA)::101 rRNAs::9, 9, 9 (5S, 16S, 23S) complete rRNAs::9, 9,…

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ASM1917534v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::08/30/2021 23:22:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,122 CDSs (total)::3,071 Genes (coding)::2,904 CDSs (with protein)::2,904 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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RNA, tRNA, circRNA: Imagine the potential of treatment!

modern When Pfizer Made history with their mRNA COVID-19 vaccine. Vaccines have sent a new era of development of mRNA therapies, and after 11.4 billion doses, mRNA therapy is the future of treatments for many different conditions. Currently, other types of RNA therapies are also attracting attention, triggering exciting new…

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ASM1863403v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/03/2021 14:29:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,407 CDSs (total)::4,307 Genes (coding)::4,183 CDSs (with protein)::4,183 Genes (RNA)::100 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7,…

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ASM1814142v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/07/2021 12:52:22 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,858 CDSs (total)::4,780 Genes (coding)::4,742 CDSs (with protein)::4,742 Genes (RNA)::78 rRNAs::6, 6, 5 (5S, 16S, 23S) complete rRNAs::6, 6,…

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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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ASM1922276v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::07/15/2021 15:46:43 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,257 CDSs (total)::8,191 Genes (coding)::8,106 CDSs (with protein)::8,106 Genes (RNA)::66 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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Exercise 8.docx – Review of Transcription and Translation – A gene encodes the instructions a cell requires to synthesize a product – rRNA is essential

Review of Transcription and Translation–A gene encodes the instructions a cell requires to synthesize a product–rRNA is essential components of ribosomes–rRNA contains code that a ribosome needs to construct a specificpolypeptide (which then folds to forms a protein)–tRNA distribute amino acids to the ribosomes–The order of codons in an mRNA…

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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

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ASM2099102v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::11/28/2021 12:10:22 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,454 CDSs (total)::3,291 Genes (coding)::3,252 CDSs (with protein)::3,252 Genes (RNA)::163 rRNAs::14, 13, 13 (5S, 16S, 23S) complete rRNAs::14, 13,…

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Solved: Briefly discuss the general organization of tRNA and rRNA …

Transfer RNA (tRNAs) are encoded for by genes. However, the tRNA is the functional end point and does not get translated into protein. tRNA genes have a promoter that recognizes and binds RNA polymerase. This initiates transcription of the tRNA. tRNA genes also have a leader and trailer sequence that…

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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

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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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ASM1890591v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::12/19/2021 14:49:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,956 CDSs (total)::2,892 Genes (coding)::2,846 CDSs (with protein)::2,846 Genes (RNA)::64 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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Mechanisms involved in the transmission of genetic diseases from mother to child

Mitochondria are the organelles that produce most of the chemical energy needed by the cell. Mitochondrial DNA (mtDNA) contains 16,569 nucleotides that can be mutated. Some of these mutations can lead to the development of mitochondrial diseases. While nuclear DNA (the well-known double helix, which encodes most of the genome)…

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Research reveals mechanism involved in transm

image: Immature mouse egg at a stage prior to ovulation, with mitochondria stained red view more  Credit: Marcos Roberto Chiaratti A research article published in the journal Science Advances describes a mechanism that helps explain how certain kinds of genetic disorders known as mitochondrial diseases are transmitted from mother to child. The study it reports…

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ASM1993088v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::09/24/2021 10:50:11 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,022 CDSs (total)::3,966 Genes (coding)::3,901 CDSs (with protein)::3,901 Genes (RNA)::56 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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Gene Set – TFDP2

Symbol Name ACBD6 acyl-CoA binding domain containing 6 ACO2 aconitase 2, mitochondrial ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif, 2 AK2 adenylate kinase 2 ALDH6A1 aldehyde dehydrogenase 6 family, member A1 AP1S1 adaptor-related protein complex 1, sigma 1 subunit AP4M1 adaptor-related protein complex 4, mu 1 subunit APH1A APH1A…

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Ch 14 assignments.docx – Chapter 14 Assignments Vocabulary 1. Transcription versus translation Transcription is the act of duplicating a gene’s DNA

Chapter 14 Assignments Vocabulary 1. Transcription versus translation Transcription is the act of duplicating a gene’s DNA sequence to create an RNA molecule, while translation is the process of converting DNA to RNA in the nucleus to produce proteins. Proteins are made from RNA copies by translation. 2. Messenger RNA…

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The rRNA directs the arrangements of amino acids to make proteins at the ribosome. (a) True (b) False.

Question: The rRNA directs the arrangements of amino acids to make proteins at the ribosome. (a) True (b) False. Translation and protein synthesis: There are three types of RNA molecules in the cell that participate in the protein synthesis mechanism. During the protein synthesis, the specific genes on the DNA…

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ASM2054021v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/15/2021 18:22:15 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,439 CDSs (total)::4,349 Genes (coding)::4,268 CDSs (with protein)::4,268 Genes (RNA)::90 rRNAs::8, 2, 2 (5S, 16S, 23S) complete rRNAs::8 (5S) partial…

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ASM1736881v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::03/11/2021 17:21:49 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,842 CDSs (total)::2,777 Genes (coding)::2,722 CDSs (with protein)::2,722 Genes (RNA)::65 rRNAs::1, 1 (5S, 16S) complete rRNAs::1 (5S) partial rRNAs::1 (16S)…

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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

1. Parte, A. C. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613-616 (2014). CAS  PubMed  Google Scholar  2. Krzyściak, W., Pluskwa, K. K., Jurczak, A. & Kościelniak, D. The pathogenicity of the Streptococcus genus. Eur. J. Clin. Microbiol. Infect. Dis. 32, 1361–1376 (2013). PubMed  PubMed…

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Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea

1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS  PubMed  PubMed Central  Google Scholar  2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….

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KEGG REACTION: R03197

    REACTION: R03197 Help Entry R03197                      Reaction                                Name Uroporphyrinogen-III carboxy-lyase Definition Uroporphyrinogen III <=> Coproporphyrinogen III + 4 CO2 Equation Reaction class Enzyme Pathway rn01110   Biosynthesis of secondary metabolites rn01240   Biosynthesis of cofactors Module M00121   Heme biosynthesis, plants and bacteria, glutamate => heme M00868   Heme biosynthesis, animals and fungi, glycine =>…

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EXAM 2.docx – EXAM 2 1 In the Stringent Response bacterial rRNA tRNA and protein synthesis temporarily cease in response to depleted nutrients in the

EXAM 21.In the Stringent Response, bacterial rRNA, tRNA, and protein synthesis temporarilycease in response to depleted nutrients in the cell. The stringent response is initiated inthe cell due to:a.an excess of aminoacyl-tRNA that accumulates due to a block in translationb.accumulation of cyclic-AMP in the cellc.metabolite inhibition of isoenzyme function in…

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ASM1584570v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Date::05/22/2015 10:24:41Annotation Method::Best-placed reference protein set; GeneMarkS+Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Provider::NCBIFeatures Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionAnnotation Software revision::2.10 (rev. 463717)Genes::5,665CDS::5,280Pseudo Genes::271CRISPR Arrays::4rRNAs::32 (5S, 16S, 23S)tRNAs::82ncRNA::1Frameshifted Genes::68##Genome-Annotation-Data-END## Read more here: Source link

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The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Escherichia coli K-12 substr. MG1655 GO:0042781

Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0042781 – 3′-tRNA processing endoribonuclease activity Synonyms: 3′ tRNA processing endoribonuclease activity, 3′ tRNase activity, tRNA 3′ endonuclease activity Definition: Catalysis of the endonucleolytic cleavage of RNA, removing extra 3′ nucleotides from tRNA precursor, generating 3′ termini of tRNAs. A 3′-hydroxy group is…

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There are 4 types of RNA: mRNA, rRNA, sRNA, and tRNA.

Home There are 4 types of RNA: mRNA, rRNA, sRNA, and tRNA. There are 4 types of RNA: mRNA, rRNA, sRNA, and tRNA. This is a List of Available Answers Options : False True The best answer is A. False. Reported from teachers around the world. The correct answer to ❝There…

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Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

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Valine tRNA levels and availability regulate complex I assembly in leukaemia

1. Rapino, F. et al. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605–609 (2018). CAS  PubMed  Google Scholar  2. Goodarzi, H. et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416–1427 (2016). CAS  PubMed  PubMed Central  Google Scholar  3. Wolfe, A….

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What is RNAcentral? | RNAcentral

RNAcentral is a database of non-coding RNA sequences that aggregates ncRNA data from over 40 member resources known as Expert Databases.1 Non-coding RNAs Similar to mRNAs, non-coding RNAs (ncRNAs) are transcribed from DNA but are not translated into proteins. NcRNAs are found in all organisms and have a broad range…

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Phylogenomic analysis confirms polyphyly of Leptospermum and delineates five major clades that warrant generic recognition – Binks – – TAXON

Leptospermum is an ecologically and economically important genus with a long unresolved taxonomic issue concerning polyphyly, as indicated from early molecular analysis on two chloroplast regions. To resolve this, we used genome skimming to obtain high-copy chloroplast and nuclear ribosomal DNA for a comprehensive phylogenomic analysis of 110 accessions comprising…

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Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium | BMC Biotechnology

1. Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, et al. Positive selection driving cytoplasmic genome evolution of the medicinally important ginseng plant genus Panax. Front Plant Sci. 2018;9:359. doi.org/10.3389/fpls.2018.00359. Article  PubMed  PubMed Central  Google Scholar  2. Takeshi T, Marouane B, Takuya I, Kazusato O, Kimiko…

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ASM648341v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/22/2018 18:06:09 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,178 CDS (total)::7,112 Genes (coding)::6,886 CDS (coding)::6,886 Genes (RNA)::66 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM296653v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/19/2021 18:16:01 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,877 CDSs (total)::1,821 Genes (coding)::1,767 CDSs (with protein)::1,767 Genes (RNA)::56 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2,…

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Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Genome organization and structure of O. laetus The MiSeq data of BTI and CBE samples of O. laetus was submitted to the NCBI SRA database under the accession numbers SRR11024516 and SRR11024517, respectively. The study was done to understand whether there exists a different species of the genus Oxycarenus similar…

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MitoVisualize: A resource for analysis of variants in human mitochondrial RNAs and DNA

Abstract We present MitoVisualize, a new tool for analysis of the human mitochondrial DNA (mtDNA). MitoVisualize enables visualization of: (1) the position and effect of variants in mitochondrial transfer RNA (tRNA) and ribosomal RNA (rRNA) secondary structures alongside curated variant annotations, (2) data across RNA structures, such as to show…

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A rRNA Expansion Segment Recruits tRNA Synthetases in Yeast

The Polacek lab discovered that a specific rRNA expansion segment of the yeast ribosome recruits three tRNA synthetases. However, deletion of this segment did neither significantly alter ribosome biogenesis & translation nor the activity of these tRNA synthetases raising the possiblity that they perfom additional functions when associated with ribosomes…

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Determine if the following statement regarding amino acid activation is true or false: Two separate enzymes are required, one to form the aminoacyl adenylate and another to attach the amino acid to the rRNA.

Question: Determine if the following statement regarding amino acid activation is true or false: Two separate enzymes are required, one to form the aminoacyl adenylate and another to attach the amino acid to the rRNA. Amino Acid Activation: If amino acids do not attach with a correct molecule of transfer…

Continue Reading Determine if the following statement regarding amino acid activation is true or false: Two separate enzymes are required, one to form the aminoacyl adenylate and another to attach the amino acid to the rRNA.

ASM305757v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::03/22/2018 17:17:07 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,149 CDS (total)::7,038 Genes (coding)::6,810 CDS (coding)::6,810 Genes (RNA)::111 rRNAs::7, 7, 1 (5S, 16S, 23S) complete rRNAs::7 (5S) partial rRNAs::7, 1…

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ASM1969325v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::08/20/2021 18:57:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,139 CDSs (total)::6,048 Genes (coding)::5,966 CDSs (with protein)::5,966 Genes (RNA)::91 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7, 6,…

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Escherichia coli K-12 substr. MG1655 tmRNA

Escherichia coli K-12 substr. MG1655 RNA Class: tmRNA Superclasses: a single-stranded RNA Instances: tmRNA Summary: The bacterial tmRNA is so-named for its dual tRNA-like and mRNA-like nature. tmRNA participates in a process mediating recovery from translation problems that result in proteins that are stalled on the ribosome. tmRNA adds a…

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rRNA Function, Location Production & Synthesis | Ribosomal RNA – Video & Lesson Transcript

What is Ribosomal RNA (rRNA)? All proteins made within the body go through the process of DNA transcription and translation. DNA transcription is the process of converting DNA into RNA. During the process of translation, the transcribed RNA is used as a genetic blueprint to convert the information into proteins,…

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NC 002528 | Virtual Laboratory Wiki

LOCUS NC_002528 640681 bp DNA circular BCT 07-JUN-2007 DEFINITION Buchnera aphidicola str. APS (Acyrthosiphon pisum), complete genome. ACCESSION NC_002528 VERSION NC_002528.1 GI:15616630 KEYWORDS . SOURCE Buchnera aphidicola str. APS (Acyrthosiphon pisum) ORGANISM Buchnera aphidicola str. APS (Acyrthosiphon pisum) Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Buchnera. REFERENCE 1 (sites) AUTHORS Shigenobu,S., Watanabe,H.,…

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ASM159282v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::03/03/2016 18:18:50 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,259 CDS (total)::3,173 Genes (coding)::3,117 CDS (coding)::3,117 Genes (RNA)::86 rRNAs::8, 6, 4 (5S, 16S, 23S) complete rRNAs::3, 1 (5S, 16S) partial…

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ASM103905v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Provider::NCBIAnnotation Date::06/19/2015 13:56:31Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Method::Best-placed reference protein set; GeneMarkS+Annotation Software revision::2.10Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionGenes::4,273CDS::4,109Pseudo Genes::61CRISPR Arrays::2rRNAs::28 (5S, 16S, 23S)tRNAs::72ncRNA::3Frameshifted Genes::15##Genome-Annotation-Data-END## Read more here: Source link

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ASM1291154v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::02/27/2020 21:08:30 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,312 CDSs (total)::2,255 Genes (coding)::2,217 CDSs (with protein)::2,217 Genes (RNA)::57 rRNAs::1, 1, 3 (5S, 16S, 23S) complete rRNAs::1, 1 (5S,…

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ASM1980304v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::08/31/2021 13:38:16 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,245 CDSs (total)::5,128 Genes (coding)::5,043 CDSs (with protein)::5,043 Genes (RNA)::117 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7,…

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ASM294953v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::01/25/2021 22:23:39 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,866 CDSs (total)::4,736 Genes (coding)::3,799 CDSs (with protein)::3,799 Genes (RNA)::130 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7,…

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An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with…

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Emerging Aspects of Jumbo Bacteriophages

Introduction Bacteriophages bearing tails with genome size beyond 200 kbp are termed jumbo bacteriophages.1 Many studies have tried to explore the new jumbo phages that infect bacteria of different species.2–7 They are also different from other bacteriophages not only because of size but also due to evolutionary path, genetic orientation,…

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ASM215354v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Provider::NCBIAnnotation Date::06/25/2014 15:11:26Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Method::Best-placed reference protein set; GeneMarkS+Annotation Software revision::2.6 (rev. 438450)Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionGenes::2,713CDS::2,629Pseudo Genes::35CRISPR Arrays::3rRNAs::3 (5S, 16S, 23S)tRNAs::45ncRNA::1Frameshifted Genes::29##Genome-Annotation-Data-END## Read more here: Source link

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ASM1330234v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::02/18/2020 23:45:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,261 CDSs (total)::4,181 Genes (coding)::4,013 CDSs (with protein)::4,013 Genes (RNA)::80 rRNAs::2, 9, 1 (5S, 16S, 23S) complete rRNAs::2 (5S) partial…

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Immune cell – ANGPTL8 – The Human Protein Atlas

ANDNOT FieldAllGene nameProtein classUniprot keywordChromosomeExternal idTissue expression (IHC)Patient ID (IHC)Tissue category (RNA)Tissue expression cluster (RNA)Reliability score tissue (IHC)Brain region category (RNA)Mouse brain category (RNA)Pig brain category (RNA)Reliability score mouse brainCell type category (RNA)Single cell type expression cluster (RNA)Cell type enrichment (RNA)Prognostic cancerCancer category (RNA)Immune cell category (RNA)Immune cell lineage category…

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ASM323668v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/22/2018 12:47:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,832 CDS (total)::2,788 Genes (coding)::2,717 CDS (coding)::2,717 Genes (RNA)::44 rRNAs:: complete rRNAs:: partial rRNAs:: tRNAs::40 ncRNAs::4 Pseudo Genes (total)::71 Pseudo Genes…

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ASM207889v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/13/2021 00:37:40 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,786 CDSs (total)::2,700 Genes (coding)::2,423 CDSs (with protein)::2,423 Genes (RNA)::86 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7, 6,…

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CD Genomics Offers NGS Services for Mitochondrial Research

New York, USA – November 26, 2021 – CD Genomics is one of the top genomics service providers in genomic research, dedicated to providing reliable services to pharmaceutical and biotech companies as well as academia and government agencies. With its high-throughput sequencing platforms, CD Genomics can provide solutions for a…

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ASM960013v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/31/2019 21:03:28 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.10 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,430 CDSs (total)::5,359 Genes (coding)::5,211 CDSs (with protein)::5,211 Genes (RNA)::71 rRNAs::2, 4, 3 (5S, 16S, 23S) complete rRNAs::2 (5S) partial…

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ASM402823v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::11/09/2020 11:04:02 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.13 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,015 CDSs (total)::2,958 Genes (coding)::2,817 CDSs (with protein)::2,817 Genes (RNA)::57 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2,…

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ASM197595v2 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::01/19/2021 11:22:08 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,922 CDSs (total)::2,866 Genes (coding)::2,843 CDSs (with protein)::2,843 Genes (RNA)::56 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2,…

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Immune cell – EPCAM – The Human Protein Atlas

ANDNOT FieldAllGene nameProtein classUniprot keywordChromosomeExternal idTissue expression (IHC)Patient ID (IHC)Tissue category (RNA)Tissue expression cluster (RNA)Reliability score tissue (IHC)Brain region category (RNA)Mouse brain category (RNA)Pig brain category (RNA)Reliability score mouse brainCell type category (RNA)Single cell type expression cluster (RNA)Cell type enrichment (RNA)Prognostic cancerCancer category (RNA)Immune cell category (RNA)Immune cell lineage category…

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ASM344421v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/16/2018 10:19:40 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,551 CDS (total)::1,516 Genes (coding)::1,452 CDS (coding)::1,452 Genes (RNA)::35 tRNAs::33 ncRNAs::2 Pseudo Genes (total)::64 Pseudo Genes (ambiguous residues)::0 of 64 Pseudo…

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ASM588728v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/04/2018 12:18:59 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,334 CDS (total)::4,229 Genes (coding)::4,072 CDS (coding)::4,072 Genes (RNA)::105 rRNAs::2, 1, 1 (5S, 16S, 23S) complete rRNAs::2, 1, 1 (5S, 16S,…

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ASM880148v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/26/2019 17:44:56 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.9 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,867 CDSs (total)::4,786 Genes (coding)::4,681 CDSs (with protein)::4,681 Genes (RNA)::81 rRNAs::8, 3, 1 (5S, 16S, 23S) complete rRNAs::7, 1, 1…

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Weill Cornell Creates New Center to Study RNA Modifications with $12M from NHGRI

[Source: CROCOTHERY/Getty Images] The National Human Genome Research Institute (NHGRI) announced Tuesday it has funded a Weill Cornell Medicine-based Center of Excellence in Genome Sciences (CEGS) to study how RNA functions to create the patterns of protein expression seen in human tissues and disease. The multi-institution CEGS will be funded…

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ASM588974v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/24/2019 21:11:27 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,858 CDSs (total)::8,784 Genes (coding)::8,478 CDSs (with protein)::8,478 Genes (RNA)::74 rRNAs::4, 6, 9 (5S, 16S, 23S) complete rRNAs::4, 1 (5S,…

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ASM194254v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/13/2016 11:55:59 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,882 CDS (total)::4,828 Genes (coding)::4,767 CDS (coding)::4,767 Genes (RNA)::54 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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Diagnostic markers of AIDS combined with TM infection

Introduction The prevalence of Human immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS) is still a public health problem that threatens the health of all human beings. According to the latest report of the World Health Organization, in the end of 2019, there were 38 million patients with human immunodeficiency virus/acquired immunodeficiency…

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ASM1066924v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/18/2021 05:39:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,292 CDSs (total)::2,220 Genes (coding)::2,142 CDSs (with protein)::2,142 Genes (RNA)::72 rRNAs::5, 4, 4 (5S, 16S, 23S) complete rRNAs::5, 4,…

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National Human Genome Research Institute fund

image: Dr. Samie Jaffrey view more  Credit: John Abbott The National Human Genome Research Institute has funded a multi-institutional Center of Excellence in Genome Sciences (CEGS), based at Weill Cornell Medicine, to develop new tools to study the major product of the human genome, called ribonucleic acid (RNA), and determine how RNA…

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ASM1312795v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/24/2021 04:36:52 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,765 CDSs (total)::4,714 Genes (coding)::4,652 CDSs (with protein)::4,652 Genes (RNA)::51 rRNAs::3, 4, 4 (5S, 16S, 23S) complete rRNAs::3, 4,…

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ASM838650v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/10/2019 04:56:21 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.9 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,450 CDSs (total)::4,361 Genes (coding)::4,332 CDSs (with protein)::4,332 Genes (RNA)::89 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2, 2…

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ASM168088v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::02/08/2016 12:05:05 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,301 CDS (total)::3,258 Genes (coding)::3,230 CDS (coding)::3,230 Genes (RNA)::43 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM280414v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/06/2020 10:23:42 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,564 CDSs (total)::1,510 Genes (coding)::1,201 CDSs (with protein)::1,201 Genes (RNA)::54 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ASM101043v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Provider::NCBIAnnotation Date::07/18/2014 14:47:57Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Method::Best-placed reference protein set; GeneMarkS+Annotation Software revision::2.6 (rev. 440435)Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionGenes::7,474CDS::7,211Pseudo Genes::167CRISPR Arrays::4rRNAs::7 ( 5S, 16S, 23S )tRNAs::87ncRNA::2Frameshifted Genes::151##Genome-Annotation-Data-END## Read more here: Source link

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ASM836527v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::04/14/2021 06:20:46 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,437 CDSs (total)::2,386 Genes (coding)::2,375 CDSs (with protein)::2,375 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ASM1239601v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/09/2020 17:56:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,425 CDSs (total)::4,369 Genes (coding)::4,275 CDSs (with protein)::4,275 Genes (RNA)::56 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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ASM789689v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/02/2019 00:38:51 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,744 CDSs (total)::7,655 Genes (coding)::7,115 CDSs (with protein)::7,115 Genes (RNA)::89 rRNAs::6, 6, 6 (5S, 16S, 23S) complete rRNAs::6, 6, 6…

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ASM991399v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::01/24/2021 03:35:51 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,857 CDSs (total)::1,783 Genes (coding)::1,749 CDSs (with protein)::1,749 Genes (RNA)::74 rRNAs::5, 5, 5 (5S, 16S, 23S) complete rRNAs::5, 5,…

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ASM286101v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::12/22/2017 13:59:43 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,796 CDS (total)::1,735 Genes (coding)::1,720 CDS (coding)::1,720 Genes (RNA)::61 rRNAs::4, 1, 4 (5S, 16S, 23S) complete rRNAs::4, 1, 1 (5S, 16S,…

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ASM1300447v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/04/2020 20:17:01 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,141 CDSs (total)::8,061 Genes (coding)::7,816 CDSs (with protein)::7,816 Genes (RNA)::80 rRNAs::4, 1, 1 (5S, 16S, 23S) complete rRNAs::4, 1, 1…

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ASM226301v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::04/19/2021 21:21:53 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,185 CDSs (total)::3,117 Genes (coding)::2,971 CDSs (with protein)::2,971 Genes (RNA)::68 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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ASM287415v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/10/2016 12:40:58 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,910 CDS (total)::4,819 Genes (coding)::4,783 CDS (coding)::4,783 Genes (RNA)::91 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::2, 1, 1 (5S, 16S,…

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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?

How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS? The info in the the 8th gff field m.ensembl.org/info/website/upload/gff.html frame – One of ‘0’, ‘1’ or ‘2’. ‘0’ indicates that the first base of the feature is the first base of a codon, ‘1’ that…

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