Matching Clinvar Reports with Optimus 5-Prime's Prediction.
Matching Sequence with Chromosome Coordinates (GRCh38).
End
Start
Chromosome
Matching 5' UTR Sequence with Gene Symbol and Transcript ID.
Resulting Sequence.
MRL Prediction
Resulting Sequence Length
In-Silico Saturation Mutagenesis
Clinvar SNVs Details
Chromosome
Position
Accession
Relative Position
Original
Mutated
Clinical Significance
Color Code
Legend
Explanation of values, fields and graphics presented in the tool.
Resulting Sequence Length
The length of query sequence.
MRL Prediction
The mean ribosome load (MRL) predicted by Optimus 5-Prime for the given query 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.
Instructions
Instructions on how to use the tool.
Matching Sequence with Chromosome Coordinates (GRCh38).
Use chromosome coordinate from GRCh38 to find out query 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. Length larger than 100nt is not permitted, the end position will automatically computed to the 100 nt downstream of start position. Click on 'Clinvar' to trigger inquiry. Resulting sequence, MRL prediction, in-silico saturation mutagenesis, and Clinvar SNVs detalis (N/A means no matching result) will be shown.
Matching 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, MRL prediction, in-silico saturation mutagenesis, and Clinvar SNVs detalis (N/A means no matching result) will be shown.