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12
BSRD: a repository for bacterial small regulatory RNA
- Nucleic Acids Res
, 2013
"... In bacteria, small regulatory non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators. They are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Recent developments in high-throughput techniques, such as genomic ..."
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In bacteria, small regulatory non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators. They are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq, have allowed ef-ficient detection and characterization of bacterial sRNAs. However, a comprehensive repository to host sRNAs and their annotations is not available. Existing databases suffer from a limited number of bacterial species or sRNAs included. In addition, these databases do not have tools to integrate or analyse high-throughput sequencing data. Here, we have developed BSRD
unknown title
, 2014
"... GenomeVISTA—an integrated software package for whole-genome alignment and visualization ..."
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GenomeVISTA—an integrated software package for whole-genome alignment and visualization
whole-genome alignment and visualization
, 2014
"... GenomeVISTA—an integrated software package for ..."
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"... GenomeVISTA – an integrated software package for whole-genome alignment and visualization ..."
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GenomeVISTA – an integrated software package for whole-genome alignment and visualization
Genome analysis Advance Access publication February 27, 2014 Accurate computational prediction of the transcribed strand of
, 2014
"... Motivation: CRISPR RNAs (crRNAs) are a type of small non-coding RNA that form a key part of an acquired immune system in prokary-otes. Specific prediction methods find crRNA-encoding loci in nearly half of sequenced bacterial, and three quarters of archaeal, species. These Clustered Regularly Inters ..."
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Motivation: CRISPR RNAs (crRNAs) are a type of small non-coding RNA that form a key part of an acquired immune system in prokary-otes. Specific prediction methods find crRNA-encoding loci in nearly half of sequenced bacterial, and three quarters of archaeal, species. These Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays consist of repeat elements alternating with specific spacers. Generally one strand is transcribed, producing long pre-crRNAs, which are processed to short crRNAs that base pair with invading nucleic acids to facilitate their destruction. No current soft-ware for the discovery of CRISPR loci predicts the direction of crRNA transcription. Results: We have developed an algorithm that accurately predicts the strand of the resulting crRNAs. The method uses as input CRISPR repeat predictions. CRISPRDirection uses parameters that are calcu-lated from the CRISPR repeat predictions and flanking sequences, which are combined by weighted voting. The prediction may use prior coding sequence annotation but this is not required. CRISPRDirection correctly predicted the orientation of 94 % of a ref-erence set of arrays. Availability and implementation: The Perl source code is freely avail-able from
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
, 2015
"... Transfer RNAs represent the largest, most ubiqui-tous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become the de facto standard for anno-tating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a por-tal for interact ..."
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Transfer RNAs represent the largest, most ubiqui-tous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become the de facto standard for anno-tating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a por-tal for interactive exploration of these gene predic-tions. Since its published description in 2009, the GtRNAdb has steadily grown in content, and remains the most commonly cited web-based source of tRNA gene information. In this update, we describe not only a major increase in the number of tRNA pre-dictions (>367000) and genomes analyzed (>4370), but more importantly, the integration of new analytic and functional data to improve the quality and bi-ological context of tRNA gene predictions. New in-formation drawn from other sources includes tRNA modification data, epigenetic data, single nucleotide polymorphisms, gene expression and evolutionary conservation. A richer set of analytic data is also presented, including better tRNA functional predic-tion, non-canonical features, predicted structural im-pacts from sequence variants and minimum free en-ergy structural predictions. Views of tRNA genes in genomic context are provided via direct links to the UCSC genome browsers. The database can be searched by sequence or gene features, and is avail-able at
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"... A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing ..."
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A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing
Article Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between
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Research Article Genome-Wide miRNA Seeds Prediction in Archaea
"... Copyright © 2014 Shengqin Wang et al.This is an open access article distributed under the Creative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Growing evidence indicates that miRNA genes exist ..."
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Copyright © 2014 Shengqin Wang et al.This is an open access article distributed under the Creative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2–8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result (
degradation and processing of RNA in Escherichia
, 2014
"... Direct entry by RNase E is a major pathway for the ..."
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