sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes

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sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes is …
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scholarly articleQ13442814

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P819ADS bibcode2010PLoSO...511970S
P356DOI10.1371/JOURNAL.PONE.0011970
P8608Fatcat IDrelease_nuemgtamkjf2ngqbpzymys6idq
P932PMC publication ID2916834
P698PubMed publication ID20700540
P5875ResearchGate publication ID45604328

P50authorHong-Yu OuQ58134583
Zixin DengQ89752891
Radhakrishnan SabarinathanQ45405948
P2093author name stringKumar Rajakumar
Kanagaraj Sekar
Narmada Sambaturu
Jayavel Sridhar
Ziauddin Ahamed Rafi
P2860cites workDeep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, HfqQ21145046
Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strainsQ24530293
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The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome bindingQ24533360
Fast and reliable prediction of noncoding RNAsQ24556645
Rfam: annotating non-coding RNAs in complete genomesQ24558580
Identification of novel small RNAs using comparative genomics and microarraysQ24601229
Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulenceQ24641915
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decayQ24669800
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targetsQ24684824
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2Q24685579
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sitesQ24806128
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loopsQ24813598
Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011Q27496618
The complete genome sequence of Escherichia coli K-12Q27860542
MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factorsQ28198553
A bioinformatics based approach to discover small RNA genes in the Escherichia coli genomeQ28205081
Novel small RNA-encoding genes in the intergenic regions of Escherichia coliQ28205853
Computational identification of noncoding RNAs in E. coli by comparative genomicsQ28216022
The RNA Molecule CsrB Binds to the Global Regulatory Protein CsrA and Antagonizes Its Activity in Escherichia coliQ28242964
Effect of RyhB small RNA on global iron use in Escherichia coliQ28275120
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesisQ28275777
Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase systemQ28291273
SseBCD proteins are secreted by the type III secretion system of Salmonella pathogenicity island 2 and function as a transloconQ28490029
Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention.Q52578211
Intergenic sequence inspector: searching and identifying bacterial RNAsQ81129525
Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coliQ82713385
Genes for small, noncoding RNAs under sporulation control in Bacillus subtilisQ28768627
Identifying DNA and protein patterns with statistically significant alignments of multiple sequencesQ29615307
A systematic survey of mini-proteins in bacteria and archaeaQ30856174
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAsQ33369087
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhiQ33483317
Regulatory roles for small RNAs in bacteriaQ34194972
Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine.Q34363246
A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genomeQ34707860
Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypesQ34971662
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptakeQ35751629
TargetRNA: a tool for predicting targets of small RNA action in bacteriaQ36749437
Small RNAs controlling outer membrane porinsQ36763357
Small noncoding RNAs controlling pathogenesisQ36769256
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomesQ37202654
Secretion and function of Salmonella SPI-2 effector SseF require its chaperone, SscBQ40533728
The RcsCDB signaling system and swarming motility in Salmonella enterica serovar typhimurium: dual regulation of flagellar and SPI-2 virulence genesQ42910457
The use of flow cytometry to detect expression of subunits encoded by 11 Salmonella enterica serotype Typhimurium fimbrial operons.Q47860468
A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutatorQ48047346
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue8
P407language of work or nameEnglishQ1860
P304page(s)e11970
P577publication date2010-08-05
P1433published inPLOS OneQ564954
P1476titlesRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes
P478volume5

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