The RNAsnp web server: predicting SNP effects on local RNA secondary structure

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

The RNAsnp web server : predicting SNP effects on local RNA secondary structure. / Radhakrishnan, Sabarinathan; Tafer, Hakim; Seemann, Ernst Stefan; Hofacker, Ivo L.; Stadler, Peter F.; Gorodkin, Jan.

In: Nucleic Acids Research, Vol. 41, 2013, p. W475-W479.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Radhakrishnan, S, Tafer, H, Seemann, ES, Hofacker, IL, Stadler, PF & Gorodkin, J 2013, 'The RNAsnp web server: predicting SNP effects on local RNA secondary structure', Nucleic Acids Research, vol. 41, pp. W475-W479. https://doi.org/10.1093/nar/gkt291

APA

Radhakrishnan, S., Tafer, H., Seemann, E. S., Hofacker, I. L., Stadler, P. F., & Gorodkin, J. (2013). The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Research, 41, W475-W479. https://doi.org/10.1093/nar/gkt291

Vancouver

Radhakrishnan S, Tafer H, Seemann ES, Hofacker IL, Stadler PF, Gorodkin J. The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Research. 2013;41:W475-W479. https://doi.org/10.1093/nar/gkt291

Author

Radhakrishnan, Sabarinathan ; Tafer, Hakim ; Seemann, Ernst Stefan ; Hofacker, Ivo L. ; Stadler, Peter F. ; Gorodkin, Jan. / The RNAsnp web server : predicting SNP effects on local RNA secondary structure. In: Nucleic Acids Research. 2013 ; Vol. 41. pp. W475-W479.

Bibtex

@article{4598a28286264fc1a25e90d491c7fd0e,
title = "The RNAsnp web server: predicting SNP effects on local RNA secondary structure",
abstract = "The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: https://rth.dk/resources/rnasnp/.",
author = "Sabarinathan Radhakrishnan and Hakim Tafer and Seemann, {Ernst Stefan} and Hofacker, {Ivo L.} and Stadler, {Peter F.} and Jan Gorodkin",
year = "2013",
doi = "10.1093/nar/gkt291",
language = "English",
volume = "41",
pages = "W475--W479",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",

}

RIS

TY - JOUR

T1 - The RNAsnp web server

T2 - predicting SNP effects on local RNA secondary structure

AU - Radhakrishnan, Sabarinathan

AU - Tafer, Hakim

AU - Seemann, Ernst Stefan

AU - Hofacker, Ivo L.

AU - Stadler, Peter F.

AU - Gorodkin, Jan

PY - 2013

Y1 - 2013

N2 - The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: https://rth.dk/resources/rnasnp/.

AB - The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: https://rth.dk/resources/rnasnp/.

U2 - 10.1093/nar/gkt291

DO - 10.1093/nar/gkt291

M3 - Journal article

C2 - 23630321

VL - 41

SP - W475-W479

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

ER -

ID: 46283922