RADAR: A web server for RNA data analysis and research

Mugdha Khaladkar; Vivian Bellofatto; Jason T.L. Wang; Bin Tian; Bruce A. Shapiro

doi:10.1093/nar/gkm253

RADAR: A web server for RNA data analysis and research

Mugdha Khaladkar, Vivian Bellofatto, Jason T.L. Wang, Bin Tian, Bruce A. Shapiro

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/ biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/bshapiro/.

Original language	English (US)
Pages (from-to)	W300-W304
Journal	Nucleic Acids Research
Volume	35
Issue number	SUPPL.2
DOIs	https://doi.org/10.1093/nar/gkm253
State	Published - Jul 2007
Externally published	Yes

All Science Journal Classification (ASJC) codes

Genetics

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10.1093/nar/gkm253

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title = "RADAR: A web server for RNA data analysis and research",

abstract = "RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/ biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/bshapiro/.",

author = "Mugdha Khaladkar and Vivian Bellofatto and Wang, {Jason T.L.} and Bin Tian and Shapiro, {Bruce A.}",

note = "Funding Information: We thank the anonymous reviewers for their constructive suggestions, which helped to improve the presentation and quality of this article. Funding to pay the Open Access publication charges for this article was provided by NCI-Frederick. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.",

year = "2007",

month = jul,

doi = "10.1093/nar/gkm253",

language = "English (US)",

volume = "35",

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journal = "Nucleic Acids Research",

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T2 - A web server for RNA data analysis and research

AU - Khaladkar, Mugdha

AU - Bellofatto, Vivian

AU - Wang, Jason T.L.

AU - Tian, Bin

AU - Shapiro, Bruce A.

N1 - Funding Information: We thank the anonymous reviewers for their constructive suggestions, which helped to improve the presentation and quality of this article. Funding to pay the Open Access publication charges for this article was provided by NCI-Frederick. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

PY - 2007/7

Y1 - 2007/7

N2 - RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/ biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/bshapiro/.

AB - RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/ biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/bshapiro/.

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RADAR: A web server for RNA data analysis and research

Abstract

All Science Journal Classification (ASJC) codes

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