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sRNATarget specifications

Information


Unique identifier OMICS_11143
Name sRNATarget
Interface Web user interface
Restrictions to use None
Input data Choose bacterial genome, choose sRNA or enter your sRNA sequence and set the score.
Computer skills Basic
Version 2.0
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for sRNATarget

sRNATarget in publications

 (12)
PMCID: 5415748
PMID: 28468647
DOI: 10.1186/s12864-017-3725-3

[…] [], pictar [], pita [], rna22 [], and rnahybrid []. in addition, there are programs designed for srna-target mrna prediction, including intarna [], coprarna [], rnapredator [], targetrna2 [], srnatarget [], and starpicker []. these models often provide candidate interactions for experimental validation. however, the main shortcoming of such models is the high false positive rate [, ]. […]

PMCID: 4782007
PMID: 27014636
DOI: 10.3389/fcimb.2016.00024

[…] the program is based on a two-step model of hybridization between an srna and a target. in comparisons with different srna target prediction tools, such as intarna, targetrna, and srnatarget, we found that starpicker performed best in both the accuracy of predicted binding sites and in identification of srna targets on an independent test dataset (ying et al., )., a 2-de […]

PMCID: 4046987
PMID: 24901988
DOI: 10.1371/journal.pone.0098813

[…] a minimum n value of 12., blast searches were performed using the integrated microbial genomes (img) webserver , using an e-value ā‰¤1eāˆ’50 as cut-off. mtvr putative targets were predicted using the srnatarget , the targetrna , and the rnapredator programs, with a cut-off of 1, a minimum seed of 7 nucleotides, and an hybridization target region window size of āˆ’100 to +30 around the translation […]

PMCID: 3976366
PMID: 24705412
DOI: 10.1371/journal.pone.0093833

[…] was cloned into ptz57r/t cloning vector (fermentas, usa) and sequenced for identification of the transcription termination site., in order to predict target mrna genes for the identified absr25, srnatarget (http://ccb.bmi.ac.cn/srnatarget/prediction.php) and intarna (http://rna.informatik.uni-freiburg.de:8080/intarna.jsp) servers were used. target genes with the score 1 in srnatarget […]

PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] algorithm, which is extended to handle the loop containing the concatenation point energetically as an external loop. tools implementing this idea are, for example, pairfold and rnacofold. the srnatarget web server, computes the mfe structure of the concatenated sequence to derive interaction features, such as length-normalized free energy, seed match length, and a/u-content […]


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sRNATarget institution(s)
Beijing Institute of Basic Medical Sciences, Beijing, China
sRNATarget funding source(s)
This work was supported by the National High Technology Development Program of China under Grant No. 2006AA02Z323, and National Sciences Foundation of China under Grants 90608004 and 30470411.

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