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sRNAPredict specifications

Information


Unique identifier OMICS_16561
Name sRNAPredict
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for sRNAPredict

sRNAPredict citations

 (20)
library_books

Genome Wide Detection of Small Regulatory RNAs in Deep Sea Bacterium Shewanella piezotolerans WP3

2017
Front Microbiol
PMCID: 5471319
PMID: 28663744
DOI: 10.3389/fmicb.2017.01093

[…] dict3/SIPHT, sRNApredict3/SIPHT are recent versions of the sRNApredict suite that are used in the efficient prediction of sRNAs, with a high level of specificity. SIPHT is a compatible web version of sRNAPredict3 that searches approximately 1900 bacterial replicons from the NCBI database and predicts putative sRNA locations. sRNApredict3 is inclusive of sequence comparable options to look for cons […]

library_books

Identification and validation of sRNAs in Edwardsiella tarda S08

2017
PLoS One
PMCID: 5340389
PMID: 28267754
DOI: 10.1371/journal.pone.0172783

[…] (2) comparative genomics, (3) ‘Orphan’ transcriptional signals and (4) ab initio methods regardless of sequence or structure similarity []. Transcriptional signal-based sRNA prediction tools include sRNApredict [], sRNAscanner [], and sRNAfinder []. sRNAPredict depends on the promoter signals, transcription factor binding sites, rho-independent terminator signals predicted by TRANSTERMHP [] and B […]

library_books

Small Regulatory RNAs of Rickettsia conorii

2016
Sci Rep
PMCID: 5105140
PMID: 27834404
DOI: 10.1038/srep36728

[…] cells when compared directly with tick vector cells, suggesting their regulation depending on the host niche. We recently predicted 126 candidate sRNAs to be encoded by R. conorii genome using SIPHT/sRNAPredict3, a web-based program based on promoter, transcriptional terminator, and RNA secondary structure prediction tools, but only five of these predicted sRNAs (MEV >2) were identified in this s […]

library_books

Bacterial small RNAs in the Genus Rickettsia

2015
BMC Genomics
PMCID: 4683814
PMID: 26679185
DOI: 10.1186/s12864-015-2293-7

[…] iomedical databases [–]. However, the presence of small, non-coding RNAs in different Rickettsia species still remains undetermined. With an aim to address this important knowledge gap, we used SIPHT/sRNAPredict2 to identify candidate novel sRNAs within the intergenic regions of all four rickettsial groups, leading to the prediction of a total of 1,785 novel sRNAs within 16 different strains repre […]

library_books

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes

2015
RNA Biol
PMCID: 4829319
PMID: 26580233
DOI: 10.1080/15476286.2015.1110674

[…] solate SF370 of the human pathogen S. pyogenes is 1852441 bp in size, of which 15% consist of intergenic regions (IGRs). Computational predictions of sRNAs in this pathogen were done previously using sRNApredict, SIPHT, sRNA scanner in SF370, MOSES in M49 GAS and sRNAPredict, eQRNA and RNAz in MGAS315. Three experimental searches for sRNAs in M1T1GAS (MGAS2221) and M49GAS using microarrays, in SF3 […]

library_books

Identification of a Novel Small Non Coding RNA Modulating the Intracellular Survival of Brucella melitensis

2015
Front Microbiol
PMCID: 4365724
PMID: 25852653
DOI: 10.3389/fmicb.2015.00164

[…] RNAs were also excluded. Promoters were identified in IGRs with pftools 2.3 with a cut-off value of 255, while terminators were identified using RNAMotif (Lesnik et al., ). Motif descriptor came from sRNAPredict (Waldor Lab, Tufts University). IGRs with both promoters and terminators were defined as containing a possible sRNA gene.Based upon these analysis criteria, a total of 21 candidate sRNA ge […]

Citations

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sRNAPredict institution(s)
Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, Boston, MA, USA
sRNAPredict funding source(s)
This work was supported by HHMI and NIAID.

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