title: STarMir: a web server for prediction of microRNA binding sites.
abstract: STarMir web server predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies (Liu,C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S. and Ding, Y. (2013). CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res., 41(14), e138). In both intra-dataset and inter-dataset validations, the models showed major improvements over established algorithms in predictions of both seed and seedless sites. General applicability of the models was indicated by good performance in cross-species validations. The input data for STarMir is processed by the web server to perform prediction of miRNA binding sites, compute comprehensive sequence, thermodynamic and target structure features and a logistic probability as a measure of confidence for each predicted site. For each of seed and seedless sites and for all three regions of a mRNA (3' UTR, CDS and 5' UTR), STarMir output includes the computed binding site features, the logistic probability and a publication-quality diagram of the predicted miRNA:target hybrid. The prediction results are available through both an interactive viewer and downloadable text files. As an application module of the Sfold RNA package (http://sfold.wadsworth.org), STarMir is freely available to all at http://sfold.wadsworth.org/starmir.html.
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: William
authors.initials: W
authors.lastname: Rennie
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: Chaochun
authors.initials: C
authors.lastname: Liu
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: C Steven
authors.initials: CS
authors.lastname: Carmack
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Wolenc
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: Shaveta
authors.initials: S
authors.lastname: Kanoria
authors.affiliation: Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Lu
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
authors.forename: Dang
authors.initials: D
authors.lastname: Long
authors.affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA yding@wadsworth.org.
authors.forename: Ye
authors.initials: Y
authors.lastname: Ding
mesh_terms: D000818:Animals; D001665:Binding Sites; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger