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RDMAS: a web server for RNA deleterious mutation analysis.

Shu W, Bo X, Liu R, Zhao D, Zheng Z, Wang S - BMC Bioinformatics (2006)

Bottom Line: RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.With a user-friendly interface, the web application is easy to use.Intuitive illustrations are provided along with the original computational results to facilitate quick analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Radiation Medicine, Beijing 100850, China. shuwj@bmi.ac.cn

ABSTRACT

Background: The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.

Results: The RDMAS web server we describe here is an online tool for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. Several structure comparison methods have been integrated; sub-optimal structures predicted can be optionally involved to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate quick analysis.

Conclusion: RDMAS can be used to explore the structure alterations which cause mutations pathogenic, and to predict deleterious mutations which may help to determine the functionally critical regions. RDMAS is freely accessed via http://biosrv1.bmi.ac.cn/rdmas.

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Related in: MedlinePlus

Web interface of RDMAS. (A) Input page. (B) Output page. (C) Online manual.
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Figure 1: Web interface of RDMAS. (A) Input page. (B) Output page. (C) Online manual.

Mentions: (iii) Difference between topological indices of RNA structures, i.e. D(R, R*) = /I(R) - I(R*)/, where I(·) represents the topological index computation functions. Several topological indices defined on the RNA tree graph representation has been presented [12,17-20]. Suggested by Merris and tested by Barash's group, the Wiener index which has been widely used in computational biochemistry has also been introduced into RNA graph [21,22] recently. There is an interesting relation [23] between the Wiener number and the Laplacian spectrum of tree graph used in RNAMute. We have also proposed and employed novel topological descriptors defined on Shapiro's coarse grained and weighted coarse grained RNA tree [24] to characterize RNA structures (details will be published elsewhere). The topological indices used in RDMAS are listed in Table 1. Detailed descriptions can be found in the online manual of the web server (Figure 1C).


RDMAS: a web server for RNA deleterious mutation analysis.

Shu W, Bo X, Liu R, Zhao D, Zheng Z, Wang S - BMC Bioinformatics (2006)

Web interface of RDMAS. (A) Input page. (B) Output page. (C) Online manual.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1574353&req=5

Figure 1: Web interface of RDMAS. (A) Input page. (B) Output page. (C) Online manual.
Mentions: (iii) Difference between topological indices of RNA structures, i.e. D(R, R*) = /I(R) - I(R*)/, where I(·) represents the topological index computation functions. Several topological indices defined on the RNA tree graph representation has been presented [12,17-20]. Suggested by Merris and tested by Barash's group, the Wiener index which has been widely used in computational biochemistry has also been introduced into RNA graph [21,22] recently. There is an interesting relation [23] between the Wiener number and the Laplacian spectrum of tree graph used in RNAMute. We have also proposed and employed novel topological descriptors defined on Shapiro's coarse grained and weighted coarse grained RNA tree [24] to characterize RNA structures (details will be published elsewhere). The topological indices used in RDMAS are listed in Table 1. Detailed descriptions can be found in the online manual of the web server (Figure 1C).

Bottom Line: RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.With a user-friendly interface, the web application is easy to use.Intuitive illustrations are provided along with the original computational results to facilitate quick analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Radiation Medicine, Beijing 100850, China. shuwj@bmi.ac.cn

ABSTRACT

Background: The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.

Results: The RDMAS web server we describe here is an online tool for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. Several structure comparison methods have been integrated; sub-optimal structures predicted can be optionally involved to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate quick analysis.

Conclusion: RDMAS can be used to explore the structure alterations which cause mutations pathogenic, and to predict deleterious mutations which may help to determine the functionally critical regions. RDMAS is freely accessed via http://biosrv1.bmi.ac.cn/rdmas.

Show MeSH
Related in: MedlinePlus