(Q35182654)

7 August 2017

title

Assessing computational tools for the discovery of small RNA genes in bacteria (English)

1 reference

7 August 2017

2

Heidi Goodrich-Blair

1 reference

7 August 2017

Xiaojun Lu

1

1 reference

7 August 2017

Brian Tjaden

series ordinal

3

1 reference

7 August 2017

language of work or name

English

0 references

publication date

18 July 2011

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7 August 2017

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7 August 2017

volume

17

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7 August 2017

issue

9

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7 August 2017

page(s)

1635-1647

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The primary transcriptome of the major human pathogen Helicobacter pylori

7 August 2017

cites work

1 reference

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Computational prediction of sRNAs and their targets in bacteria.

13 July 2018

1 reference

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A broadening world of bacterial small RNAs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

13 July 2018

1 reference

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RNAz 2.0: improved noncoding RNA detection.

13 July 2018

1 reference

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Experimental approaches for the discovery and characterization of regulatory small RNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

The Listeria transcriptional landscape from saprophytism to virulence.

13 July 2018

1 reference

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Regulatory RNAs in bacteria

13 July 2018

1 reference

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Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Rfam: updates to the RNA families database

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Clustal W and Clustal X version 2.0

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Identification of small RNAs in diverse bacterial species

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Identifying bacterial genes and endosymbiont DNA with Glimmer

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Fast and reliable prediction of noncoding RNAs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

Noncoding RNA gene detection using comparative sequence analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

RNAMotif, an RNA secondary structure definition and search algorithm

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

SSAHA: a fast search method for large DNA databases

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3162329

13 July 2018

Identifiers

DOI

10.1261/RNA.2689811

1 reference

7 August 2017

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7 August 2017

1 reference