Reading the output

Reading the output

Textual output

The text output simply presents the list of genes predicted with possible partial genes on the border of the sequence and possible frameshifts. For each region predicted, you can read the beginning, the end and the coding phase of the coding region predicted.

• partial genes are indicated by a '>' (beginning of the sequence) or a '>' (end of the sequence).
• each predicted frameshift is indicated by a vertical bar '|' at the end and beginning of each region.

Using the first example sequence available on the web, a noisy high GC content sequence with 'N's, selecting the correct organism (Ralstonia) and a frameshift penalty of 8 (for low quality sequences), we get the following prediction:

 Start End Ph. 
    148  911   1 |
 |  912 1181  3
   1254 1387  3 > 

A first gene is predicted on phase 1, from 148 to 1181 interrupted by a predicted frameshift between position 911 and 912. Then a partial gene starts at 1254 on phase 3.

Graphical output

As an illustration, Figure * presents the graphical output obtained using the same GC rich and noisy sequence provided as example 1 on the web interface, using the correct "Ralstonia" model with default parameters and the default frameshift penalty set to 8 (for a low quality sequence).

• The horizontal axis is the sequence (here 1387 nuc. long).

• The vertical axis represents the 6 possible coding phases (+1,+2,+3 for the direct strand, -1, -2,-3 for the reverse) and possible non coding (IG stands for intergenic) regions. Each of these is called a track in the rest of the document. Each of these possible prediction is called a track in the sequel.

• On the 6 coding tracks, small red bars represent occurrences of STOP codons, blue bar represent START codons. The wider the blue bar, the better the start is (according to the presence of RBS, the type of the codon and how degenerated the codon is in the sequence eg. NNN is a possible start, but it is very degenerated).

• The fine black curve is a smoothed, normalized score of the coding/non coding likelihoods over a sliding window. The window width can be controlled in the "Output parameters" to increase or lower the smoothing (this does not change the prediction)

• The light green curves indicates the GC% and the GC3% of the sequence. The GC% is indicated in the non coding track (IG) and is artificially amplified: the track contains variations from 25% to 75% GC. The GC3% indicates the percentage of GC bases in the 3rd position of the codons in this phase. It is not amplified (the track contains variation from 0% to 100%).

• The large red blocks indicate the prediction of FrameD. Thin red lines that connect two blocks indicate predicted frameshifts.

• When activated, light gray and magenta lines will indicate a mean (expected) prediction beyond the optimal one.

  On the above image, one can observe here, between 100 and 150 that FrameD hesitates between the two possible start codons: a non negligible part of the predictions would actually use the second START but the first is preferred. Another position of doubt is in the 700 region where the uncertainty on coding phase is clear: two frameshifts around 650 and 750 roughly could explain the increase in coding score in phase 2. Despite the fact that many suboptimal prediction actually predict these 2 frameshift, the optimal prediction does not.

  These two possible frameshifts are also visible on the central magenta line which represent an amplified frameshift expectation based on all possible predictions. We see a possible insertion around 650 (up curve) and a possible deletion around 750 (down curve).

  A frameshift is actually predicted around 900, close to the N stretch, close to where we created it.

We can get back to the initial page and ask for a corrected sequence and resubmit it for analyze, using the same frameshift penalty of 8 (for low quality). The corresponding graphical output is visible in Figure *.

 Start End Ph. 
  148 1182 1 
 1255 1388 1 >

No frameshift is predicted anymore.

Reading the output