<home> DMMPMM project - some additional information

Nucleotide probabilities (in order A,C,G,T) computed over Drosophila dmel40 genome release: 1-strand, 2-strand.

Bergman set has two PWMs for Dl factor. We used dl-A motif becase it shows better quality in all of the cases. PWM ROC curves graph can be found here.

Noyes set containts two sequence-sets for Bcd factor. We took the one corresponding to the better quality motif. The other one is actually presented in the Noyes_hd set.

• All motif logos presented on this site are made by pmflogo tool in two modes. The first one (red grid) corresponds to the cases where it wasn't possible to use DIC as scaling (for Bergman and Down sets we do not know the number of aligned sequences). The second one (green grid) refers to DIC usage.
• For Bigfoot motifs (see any motif-specific page in the Bigfoot motif list) you can check llib.yaml file. It contains all technical program input parameters and results in human-readable YAML format.

All 'ready'-motifs logos in comparison sheets are scaled according to the total footprints number (not counting the small number of absent sites). It has no real effect on visual representation.

Ytilib uses 'Statistics2' ruby library by Shin-ichiro HARA <link>.