The Sequence Read Archive

Leinonen, Rasko; Sugawara, Hideaki; Shumway, Martin

doi:10.1093/nar/gkq1019

Cited by 2,402 publications

(1,893 citation statements)

References 9 publications

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“…Libraries were downloaded from NCBI Sequence Read Archive (SRA) [82] and converted to FASTQ format using either SRAdb v1.40.0 [83] or fastq-dump v2.8.2 [82]. We preprocessed paired-end and single-end libraries using Trimmomatic v0.36 [84] in order to trim known adapters and/or low quality ends.…”

Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

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Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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“…Mining public databases to elucidate the distribution of the 'Diapherotrites' in nature We attempted to identify the occurrence of members of the CP-'Diapherotrites' in various ecosystems by mining metagenomic data sets in the IMG database (n ¼ 893, accessed in December 2013), Sangergenerated 16S rRNA gene sequences in the nr database (n ¼ 53 65 062 sequences, accessed in January 2014) and partial, high-throughput (pyrosequencing and Illumina)-generated archaeal 16S rRNA gene sequences in MG-RAST (Meyer et al, 2008) and SRA archive (Leinonen et al, 2011) (n ¼ 31 972 882 sequences in 775 data sets generated using archaeal primers). Identification of CP-'Diapherotrites' in metagenomic data sets was conducted using the three 'Diapherotrites' SAG assemblies for anchoring metagenomic reads as previously described (Rinke et al, 2013).…”

Section: Principal Component Analysis (Pca)mentioning

confidence: 99%

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

et al. 2014

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The archaeal phylum ‘Diapherotrites’ was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the ‘Diapherotrites’. The most complete of the SAGs, Candidatus ‘Iainarchaeum andersonii’ (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the ‘Diapherotrites’ have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. ‘Diapherotrites’ 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.

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“…In this article I describe an approach how it is possible to process ChIP-seq data from different experiments automatically, starting either from the SRA format files from NCBI [2], or FASTQ format files, or BAM format files which contain aligned reads. Among the many different available genome alignment tools I use the BWA.…”

Section: Introductionmentioning

confidence: 99%

Command line analysis of ChIP-seq results

Barta

2011

EMBnet j.

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The Sequence Read Archive

Cited by 2,402 publications

References 9 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

Command line analysis of ChIP-seq results

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