ApolloRNA imageUser Guide

ApolloRNA 1.11.3a (February 17, 2010) provides some extensions for Apollo 1.11.3 related to non protein coding RNA identification:

To get more information about Apollo, see the Apollo User guide.
Examples data files: NC_000868.xml (Pyrococcus abyssi Genbank annotations), NC_000868_mfe150.txt (Pyrococcus abyssi free energy on a 150 nucleotides sliding window)


Enabling RNA menu
The RNA menu is automatically enabled when required external softwares are launchable on the computer.
Secondary structure prediction (first item) is activated if RNAfold (Vienna RNA package) and convert (ImageMagick) are launchable.
RNA/RNA interaction search (second item) is actived if RNAfold and RNAeval (Vienna RNA package) are launchable.
Go to Download page of ApolloRNA web site, for a detail download and install protocol of these softwares.


Computing and viewing predicted secondary structure of a selected sequence
This extension allows the computing and the visualization of the secondary structure of a subsequence, predicted with RNAfold. The user can save it in a image file. convert program of ImageMagick is used to translate the image generated by RNAfold to GIF format image and to flip the image. Note that this functionality is not available if no sequence is loaded in Apollo or if the length of the selected sequence is higher than 1 500 nt.
Description
Select a feature or a sequence, open RNA menu and select "Secondary structure compute...". A window opens (see below). The free energy of the predicted structure is displayed on the right. Note that if more than one sequence are selected, only the structure of the first sequence is computed.

secondary structure window
Options

Searching and viewing RNA/RNA interactions
A request sequence is defined and research genomic regions are scanned to find potential RNA targets of the request sequence. Note that this functionality is not available if no sequence is loaded in Apollo or if the "Reverse complement" option is checked.
Search RNA/RNA interactions
Viewing RNA/RNA interactions
When the research is achieved, a new window opens (see below) with a table listing the predicted targets of the request sequence.

result interaction research window

The table presents one target per line with the following description of each column:

Position: low genomic position,
St: strand,
Interaction: interaction visualization, (The target is painting in red, the request sequence in blue)
Clicking on the picture opens a new window to better see the interaction,
Prev: preceeding gene and its distance with overlapping gene(s),
Gene Pos: low genomic position of overlapping gene(s),
Gene: overlapping gene(s),
Gene Desc: description of overlapping gene(s) product, and in parentheses the related comments when the product is an hypothetical protein. In a Genbank file, the gene product is contained in its qualifier "/product" and the related comments in the qualifier "/Note".
Next: following gene and its distance with overlapping gene(s),
Strands: respectively, strands of the previous gene, overlapping gene(s) and the next gene, ('>' for strand +, '<' for strand - and '.' when no value)
L: length of the interaction,
Var1: main variable of the search method (the one of the fold based method is the interaction free energy computed by RNAeval, the one of the alignment based method is the score of the alignment),
Var2: secondary variable of the search method (the one of the fold based method is the RNAfold free energy),
: order number according to the search method,
Pos N°: order number according to the genomic position.

Click the "Save to text" button to save the interactions in a text file.
Click the "Save to fasta" button to save the target sequences in a multiple-fasta file.
Click the "Save to GFF" button to save the targets in a GFF file.
Click on an interaction picture: a new window opens (see below). Click the "Save image as..." button to save the interaction visualization as a PNG file.

View interaction window

The two previous windows contain a "Configure visualization" button, that allows to modify the characters linking two paired nucleotides in the visualization.
Configure window

Visualizing quantitative variables all along the loaded sequence
Apollo users could only display the graph of "GC%" variable on a sliding window. This extension allows the visualization of up to five additional graphs on Apollo's main window. These graphs could be based on internal computed values or from other software outputs.
Description

Example
This is a view of one loaded variable and one computed one:

Five graphs on Apollo window

Getting information on selected sequence(s)
This extension allows to get information: on selected sequence(s) and the entire loaded sequence.

Description
Select a feature or a sequence, or several ones, open Analysis menu and select "Selected sequence information...". A window opens (see the window below where two tRNAs are selected).

Information window on selected sequences (here two tRNAs)
Options

Exporting chained views of a user-defined sub-sequence

Apollo users could only print in a file the current view of the main Apollo window. This extension allows the export in files of a set of chained views of a subsequence. The user enters the positions of a subsequence, a zoom factor and calls the export: a set of image files is created. The images are ordered, zoomed and chained views of the subsequence.
Description

export image dialog
Options

Click the "Compute number of files" button to know the number of files, which will be created according to the current parameters.
Results

Created images are chained zoomed views of the subsequence which starts and stops at the specified positions. Overlapping value determines the number of nucleotids displayed in both consecutive views. Created images are PNG files ; their name is the entered file name, followed by the character "_" and the number of the view.
Example

The genomic sequence of Pyrococcus abyssi GE5 (1 765118 nt) is loaded in Apollo. The export of a subsequence starting to the position 198 000 and stopping to 210 000, with a zoom factor equals to 200.0, with 1 000 overlapping nucleotids in files whose name is prefixed by "NC000868" is loaded. 2 image files are created: NC000868_1.png and NC000868_2.png (see below). Note that the last image, NC000868_2.png, doesn't finish to the stop position, but "contains" the stop position.

view window          view window

Last update: February 17, 2010.