Nucleic Acid Phylogenetic Profile
Names
More detailed information about this field from each metasource.
Nucleic Acid Phylogenetic Profile
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
NAPP
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
napp
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
Names
More detailed information about this field from each metasource.
Nucleic Acid Phylogenetic Profile
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
NAPP
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
napp
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
Names
More detailed information about this field from each metasource.
Nucleic Acid Phylogenetic Profile
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
NAPP
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
napp
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments.
Description
More detailed information about this field from each metasource.
NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments.
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Nucleic Acid Phylogenetic Profile database
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
Webpage:
http://napp.u-psud.frWebpage
More detailed information about this field from each metasource.
http://napp.u-psud.fr
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://rna.igmors.u-psud.fr/NAPP
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://napp.u-psud.fr/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
Licence:
Name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States (CC BY-NC-ND 3.0 US)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States (CC BY-NC-ND 3.0 US)
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by-nc-nd/3.0/us/
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
PMID: 19237465
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
NAPP: the Nucleic Acid Phylogenetic Profile Database
PMID: 21984475
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
http://dx.doi.org/10.1093/nar/GKR807
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
PMID: 19237465
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
NAPP: the Nucleic Acid Phylogenetic Profile Database
PMID: 21984475
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
http://dx.doi.org/10.1093/nar/GKR807
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
PubMed citations: 40.
40 articles citing: Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications. PMID:35806357
Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus. PMID:31911464
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. PMID:29986060
Assessment of Bona Fide sRNAs in Staphylococcus aureus. PMID:29515534
Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3. PMID:28663744
Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis. PMID:28348860
Characterizing the transcriptional adaptation of Staphylococcus aureus to stationary phase growth. PMID:27162210
Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PMID:27035918
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus. PMID:26861020
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae. PMID:26024923
SRD: a Staphylococcus regulatory RNA database. PMID:25805861
Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. PMID:25364802
Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions. PMID:25313390
Small regulatory RNAs from low-GC Gram-positive bacteria. PMID:24576839
A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. PMID:24557948
Dual RNA regulatory control of a Staphylococcus aureus virulence factor. PMID:24510101
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. PMID:23941402
Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure. PMID:23733475
Exploration of noncoding sequences in metagenomes. PMID:23536879
Predicting sRNAs and their targets in bacteria. PMID:23200137
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus. PMID:23097430
The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection. PMID:22629378
An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains. PMID:22139924
The modulation of Staphylococcus aureus mRNA turnover. PMID:22004033
NAPP: the Nucleic Acid Phylogenetic Profile Database. PMID:21984475
Assessing computational tools for the discovery of small RNA genes in bacteria. PMID:21768221
CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers. PMID:21532344
The Staphylococcus aureus RNome and its commitment to virulence. PMID:21423670
A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis. PMID:21266481
Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application. PMID:21255362
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. PMID:20920266
A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PMID:20532214
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. PMID:20511587
Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PMID:20505759
Missing genes in the annotation of prokaryotic genomes. PMID:20230630
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. PMID:20230605
Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. PMID:20181675
Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. PMID:20151104
An overview of RNAs with regulatory functions in gram-positive bacteria. PMID:19859665
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. PMID:19786493 -
NAPP: the Nucleic Acid Phylogenetic Profile Database
PubMed citations: 9.
9 articles citing: NAPP: the Nucleic Acid Phylogenetic Profile Database
Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. PMID:29551268
Assessment of Bona Fide sRNAs in Staphylococcus aureus. PMID:29515534
PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PMID:28875072
Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3. PMID:28663744
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. PMID:26614125
Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions. PMID:24884623
Bioinformatics of prokaryotic RNAs. PMID:24755880
Computational small RNA prediction in bacteria. PMID:23516022
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus. PMID:23097430 - http://dx.doi.org/10.1093/nar/GKR807
Tags:
Tags
More detailed information about this field from each metasource.
clustering
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
non-coding rna
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence
metasource: Fairsharing.org
version: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
nucleic acids
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
nucleic acid structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:22.646884
Tags
More detailed information about this field from each metasource.
clustering
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
non-coding rna
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: NAPP; Nucleic Acid Phylogenetic Profile; DOI: https://doi.org/10.25504/FAIRsharing.vr52p3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
functional, regulatory and non-coding rna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
nucleic acid sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
nucleic acids
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
nucleic acid structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:22.646884
clustering non-coding rna rna sequence rna sequence functional, regulatory and non-coding rna structure prediction nucleic acid sites, features and motifs nucleic acids nucleic acid structure analysis
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