RNALogo - a new approach to display structural RNA alignment

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☞ Input formats
 ☞ Ouput format settings
 ☞ Advanced settings
 ☞ Result explanation

☞ Manipulation of using Adobe SVG viewer

► Accept four different kinds of input formats:



► Output format settings:
 
► Advanced settings :

►Start/End position number :

The numerical label of the first and last nucleotide in the multiple sequence alignment. User could specify the interesting region to create logo.

►Mutual Information :

Mutual information is a convenient measure of the non-independence between two positions (Gutell et al., 1992). The mutual information, Mij , between two positions, i and j, is symmetrical and the mutual information is only calculated between the base-paired regions. If the pairing occurs together with total sequence conservation, the mutual information is zero. If the base pairings without sequence conservation means that there is mutual information and a signal is displayed.

►Frequency plot :

Show the residue frequencies, rather than information content.

►Perfectly conserved base pairs :

If all nucleotides in two particular positions of alignment are base-paired, this base pairs is called 'perfectly conserved base pairs' and  will be drawn in specified color (see figure below).

►Perfectly conserved nucleotide :

If the nucleotide in particular positions of alignment is conserved, this nucleotide is called the 'perfectly conserved nucleotide' and  will be drawn in specified color (see figure below).

►Pseudoknot annotation :
    Annotate the pseudoknot interaction regions by using two color lines by the side of specified positions.

► Result explanation:

►Thickness of base pair line :
    The thickness of line reflects the pairing ratio directly, i.e. the thicker line, the higher pairing ratio.

►Solid gray line :
    The solid gray line means the pairing ratio is between low conserved base pair and highly conserved base pair.
► Manipulation of using Adobe SVG viewer:

►Navigating :

▪ Panning: Hold the 'Alt' key and click-and-drag with the mouse to pan an SVG image. When the scroll lock is enabled and Adobe SVG Viewer has the focus, the arrow keys may be used to pan the image.

▪ Zooming: Hold the 'Ctrl' key and click to zoom in at the mouse pointer location. Hold the control key and click-and-drag to select a region to zoom into. Hold the control and shift keys and click to zoom out. You can also use the zoom commands in the context menu.

►Using the contextual pop-up menu :

Right-click in the SVG image area to open the contextual pop-up menu. This will reveal the commands and options for interacting with the SVG image.

▪ Links: If you bring up the context menu over a link, you can choose Open or Open in New Window to activate the link.

▪ Quality: You can disable the Higher Quality option to cause the SVG image to display more quickly, but with lower quality.

▪ Searching: Click Find to open the find dialog box. Here you may enter the text you want to search for, make choices about matching whole words only, case, and the direction of the search. The find command works with transparent, obscured, or moving text. The entire document is searched, regardless of how much of the SVG is currently visible. The result of the search is highlighted, and panned (but not zoomed) into view.

▪ Copying: The Copy SVG and Save SVG as commands let you copy the SVG image to the clipboard and save the image to a local file. The copy command places the SVG as it currently appears onto the clipboard in both Unicode and raster formats. Note that this differs from the Save SVG as command, which makes a copy of the original SVG file. When text is selected, the copy command changes to Copy Selected Text.

Department of Computer Science and Information Engineering, National Central University, Tao-yuan, Taiwan
Contact with site administrator: Tzu-Hao Chang