RNAstrand web server

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The RNAstrand web server predicts the reading direction (plus or minus strand) of a structured RNA in a multiple sequence alignment.

Simply paste or upload your ClustalW sequence alignment below and click Proceed. To get more information on the meaning of the options click the symbols or read the help pages. You can test the server using this sample alignment.

Paste your input alignment here:

[clear]

Or upload a file:

Paste the REVERSE complement of your alignment here (leave blank to calculate the REALIGNED reverse complement of your input alignment automatically!)

[clear]

Or upload a file:

Basic options

	Cutoff c RNAstrand reports a score D which converges to +1 the larger the evidence that the RNA is found in the reading direction of the input alignment and to -1 the larger the evidence that the RNA is found in the reverse complement of the input alignment. The strand classification is reported according to a user defined threshold value c, i.e. D>+c: RNA is in reading direction of input alignment; D<-c: RNA is reverse complement of input alignment; -c<=D<=+c: No decision.
	Score the whole alignment Specifies if whole alignment is regarded.
	Score only a user-defined subregion Specify a subregion of the alignment for which strand prediction will be carried out.
	from to

Notification via e-mail upon completion of the job (optional):