The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Open accessAbstract
CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de.
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Cites
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Busch, A., Richter, A. S., & Backofen, R. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn544 · Cited by 552
Cited by
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Mann, M., Wright, P. R., & Backofen, R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx279 · Cited by 725
Orlandini von Niessen, A. G., Poleganov, M. A., Rechner, C., Plaschke, A., Kranz, L. M., Fesser, S., Diken, M., Löwer, M., Vallazza, B., Beissert, T., et al. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2018.12.011 · Cited by 365
Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
Iosub, I. A., van Nues, R. W., McKellar, S. W., Nieken, K. J., Marchioretto, M., Sy, B., Tree, J. J., Viero, G., & Granneman, S. (2020) · eLife · doi:10.7554/elife.54655 · Cited by 98
sRNA-controlled iron sparing response in Staphylococci
Coronel-Tellez, R. H., Pospiech, M., Barrault, M., Liu, W., Bordeau, V., Vasnier, C., Felden, B., Sargueil, B., & Bouloc, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac648 · Cited by 43
“Putative IsrR targets were found by CopraRNA (32) set with default parameters and isrR orthologs from S. aureus NCTC8325 (NC_007795), S. epidermidis RP62A (NC_002976), S. lugdunensis HKU09-01 (NC_013893), Staphylococcus pseudintermedius HKU10-03 (NC_014925), Staphylococcus pseudintermedius ED99 (NC_017568), Staphyloco…”
BackgroundMethodInfluentialGerovac, M., Wicke, L., Chihara, K., Schneider, C., Lavigne, R., & Vogel, J. (2021) · mBio · doi:10.1128/mbio.03454-20 · Cited by 40
Metadata
- Authors
- Wright, P. R., Georg, J., Mann, M., Sorescu, D. A., Richter, A. S., Lott, S., Kleinkauf, R., Hess, W. R., & Backofen, R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-05-16
- Volume
- 42
- Issue
- W1
- Pages
- W119-W123
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2144723744
- Cited by
- 364
- References
- 2
- FWCI
- 10.95
- Type
- journal article
- Language
- en
- Open access
- gold
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- Wright, P. R., Georg, J., Mann, M., Sorescu, D. A., Richter, A. S., Lott, S., Kleinkauf, R., Hess, W. R., & Backofen, R. (2014). CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Research. https://doi.org/10.1093/nar/gku359
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