Explanation of values, fields and graphics presented in the tool.
Length
The length of input sequence.
MRL
The mean ribosome load (MRL) predicted by Optimus 5-Prime for the given input sequence for length range in 25 to 100 nt. Input sequence shorter than 25 nt is not allowed and input sequence longer than 100 nt will be truncated from most 3' (closer to start codon) to 5'.
Fold change(log2)
The log2-transformed fold change of MRL for each pair of SNV of wild-type sequence: log2(SNV MRL/WT MRL).
Heatmap color and value
The log2-transformed fold change is depicted as blue/red color intensities in the heatmap. Negative value (blue) indicates that this SNV brings MRL down compared to input sequence and positive value (red) indicates that this SNV increases MRL compared to input sequence.
Largest positive/negative fold change (log2)
The most positive log2-transformed fold change value is shown from the in-silico saturation mutagenesis heatmap, and the position and the specific mutation of that SNV is shown in red font color. This means that the SNV brings the biggest effect on increasing MRL for the input sequence. The most negative log2-transformed fold change value, together with the SNV's position and mutation is shown in blue, and this means that the SNV brings the biggest effect on decreasing MRL for the input sequence.
Instructions
Instructions on how to use the tool.
Input Sequence with Chromosome Coordinates (GRCh38).
Use chromosome coordinate from GRCh38 to find out input sequence. Chromosome number, +/- strand (+ strand in default), start and end position all need to be filled in. '+ 100' button can be used to directly compute 100 nt downstream end position given the start position. Click on 'Search' to trigger inquiry. Resulting sequence will be shown in the large type-in box.
Input Sequence with Gene Symbol and Transcript ID.
Search for gene of interest in the dropdown menu and pick the specific transcript ID from that gene. Resulting sequence will be shown in the large type-in box.
Directly Type In 5' UTR Sequence.
5' UTR sequence can be directly typed into the large type-in box. Press 'Predict' button to generate prediction including MRL value and in-silico saturation mutagenesis.
Filter on SNVs' Scores.
Select the direction of filtering first, and type in the threshold value. For example, if 'higher than' was selected, and '0' was put in as the threshold value, press 'Filter' button, then the list of SNVs containing position and mutation information, which produce log2-transformed fold change value higher than 0, will pop up in the box below.
Sort by Fold Change / SNV Position.
The list order is sorted by fold change in default. When the direction selection is 'higher than', the list was sorted from the largest SNV score to lowest, when the direction selection is 'lower than', the list was sorted from the most negative SNV score (biggest absolute value) to least negative SNV score. The list order can be changed by click on 'Sort by SNV Position', then the list will be ordered from the most 3' position (closet to start codon) to the most 5' position.