Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database.
2016-07-01 | GSE80057 | GEO
Project description:Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database. Transcriptome profiling of the aerial-tissues and the roots of Swertia japonica
2016-07-01 | E-GEOD-80057 | biostudies-arrayexpress
Project description:De novo Bacterial whole genome sequencing
| PRJNA768977 | ENA
Project description:Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. Ribo-seq next generation sequencing technique that provides a genome-wide snapshot of the position translating ribosome along an mRNA at the time of the experiment. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds to screen for spurious ORFs based on a growth curve model. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel ORFs including variants of previously annotated and novel small ORFs (<71 codons). Our predictions were supported by matching mass spectrometry (MS) proteomics data and sequence conservation analysis. REPARATION is unique in that it makes use of experimental Ribo-seq data to perform de novo ORF delineation in bacterial genomes, and thus can identify putative coding ORFs irrespective of the sequence context of the reading frame.
2017-08-03 | PXD005901 | Pride
Project description:Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. Ribo-seq next generation sequencing technique that provides a genome-wide snapshot of the position translating ribosome along an mRNA at the time of the experiment. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds to screen for spurious ORFs based on a growth curve model. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel ORFs including variants of previously annotated and novel small ORFs (<71 codons). Our predictions were supported by matching mass spectrometry (MS) proteomics data and sequence conservation analysis. REPARATION is unique in that it makes use of experimental Ribo-seq data to perform de novo ORF delineation in bacterial genomes, and thus can identify putative coding ORFs irrespective of the sequence context of the reading frame.
2017-08-09 | PXD005844 | Pride
Project description:DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.
2022-05-12 | GSE184372 | GEO
Project description:DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.
2022-05-12 | GSE184373 | GEO