Compute mean expected prediction: if selected, FrameD will not only compute an optimal prediction but will also compute a iomeanli prediction. This is especially useful for frameshift detection: it may be the case that the optimal prediction does not contain frameshifts but that many suboptimal prediction may contain one. This mean prediction appears in the graphical output (see Figure 1).

Frameshift penalty can be changed (default value is 12). Lower penalties increase the probability that a frameshift will be predicted and are well suited eg. to EST analysis.

Stop penalty can be changed (default value is 4). Lower penalties allow the prediction of smaller genes.

Increased sensitivity penalizes intergenic region which articially increases FrameD sensitivity. This can be useful to analyze sequences with non standard coding statistics (eg. containing gene obtained through lateral transfers) and which are usually visible in FrameD graphical interface as open reading frames with an unstable coding potential.

BlastX pseudo-count indicates to what entent existing similarity information can increase the coding score in the hit frame. The default value of 0 allows to plot similarities in the graphical output without in uencing the prediction. Typical values range from 1.0 to 5.0 (See FrameD documentation available as Supplementary Material). as local GC% and GC3%. This is illustrated in Figure 1where FrameD has been applied to a genomic sequence of Ralstonia solanacearum modi ed to highlight FrameD features. Learning models for new organisms

Generate corrected/translated sequence tells FrameD to respectively produce a sequence where predicted frameshifts are corrected and/or proteic sequences which are translations of the predicted coding regions (only genes with no frameshifts are translated). These sequences are available as links in the result page.

Matured eukaryotic sequence analysis limits START codons to ATG, deactivates the RBS code, change a priori probabilities of being coding or not and disables gene overlapping.

TGA is not a STOP codon should be activated for the analysis of sequences from organisms that uses a non standard genetic code where TGA codes for an amino-acid. Also available on the page for learning new probabilistic models for new organisms.

RBS pattern indicates the RBS pattern used for RBS detection. The default value is ATTCCTCCA from E. Coli.