Biocomputational prediction of small non-coding RNAs in Streptomyces (Q21263182)

19 August 2022

Josef Pánek

Josef

Pánek

1 reference

19 August 2022

Jan Bobek

series ordinal

author given names

Jan

author last names

Bobek

1 reference

19 August 2022

Karel Mikulík

series ordinal

author given names

Karel

author last names

Mikulík

1 reference

19 August 2022

Jirí Vohradský

series ordinal

author given names

Jiří

author last names

Vohradský

1 reference

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

19 August 2022

language of work or name

English

0 references

publication date

2008

0 references

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217

0 references

cites work

1 reference

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Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

19 March 2017

1 reference

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Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2

19 March 2017

1 reference

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Identification of cyanobacterial non-coding RNAs by comparative genome analysis

19 March 2017

1 reference

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sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Rfam: annotating non-coding RNAs in complete genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Identification of novel small RNAs using comparative genomics and microarrays

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Basic local alignment search tool

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Primer3 on the WWW for general users and for biologist programmers

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Global analysis of small RNA and mRNA targets of Hfq

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Computational identification of noncoding RNAs in E. coli by comparative genomics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

6S RNA regulates E. coli RNA polymerase activity

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Prediction of structural noncoding RNAs with RNAz

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

How to find small non-coding RNAs in bacteria

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Structure and functional properties of prokaryotic small noncoding RNAs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Prediction of rho-independent transcriptional terminators in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Small RNAs in Escherichia coli.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Rho and RNA: models for recognition and response

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Computer assisted identification and classification of streptomycete promoters

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Characterization of the alternative sigma factor sigmaG in Streptomyces coelicolor A3(2).

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

RNA consensus structure prediction with RNAalifold

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Cascade of sigma factors in streptomycetes: identification of a new extracytoplasmic function sigma factor sigmaJ that is under the control of the stress-response sigma factor sigmaH in Streptomyces coelicolor A3(2).

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Rho-dependent termination of transcription is governed primarily by the upstream Rho utilization (rut) sequences of a terminator

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2422843

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18477385

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-9-217

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2571183

https://scigraph.springernature.com/pub.10.1186/1471-2164-9-217

1 reference

9 September 2019

OpenCitations bibliographic resource ID

2571183

1 reference