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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

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Publication for sRNAPredict

sRNAPredict in publications

 (24)
PMCID: 5471319
PMID: 28663744
DOI: 10.3389/fmicb.2017.01093

[…] conserved and thermodynamically stable rna secondary structures in multiple sequence alignments.rnaalifold, a software used for the prediction of a consensus structure for a set of related rnas.srnapredict3/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 […]

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

[…] (data unpublished) and e. tarda ebi202 (accession no. cp002154.1) were chosen for in silico prediction. the computational methods were applied for the prediction of srnas including srnascanner and srnapredict3. srnapredict3 identified srnas based on intergenic conservation and rho-independent terminators in the closely related bacterial genomes. srnascanner computes the locations […]

PMCID: 5225090
PMID: 28123382
DOI: 10.3389/fmicb.2016.02160

[…] finding vrp as a possible srna target. this prediction was complemented with another tool, rnahybrid, to authenticate the pairing region between vrra and vrp (). another tool is the software package srnapredict. used this program to identify the srna micx. this srna negatively regulates the expression of vc0972, which encodes an uncharacterized omp, and vc0620, which encodes the periplasmic […]

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 […]

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

[…] 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 […]


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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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