Functionality: Service calculates the frequency of modified nucleosides at each position for a given set of tRNA sequences and visualizes the results. Aligned tRNA sequences derived from the MODOMICS database constitute the input for the program.
1. tRNA sequences can be selected according to kingdom, species, cellular localization (organelle) and/or amino acid specificities or individually from the provided list.
2. After clicking the "Draw modification profile" the profile is displayed in the framework of the cloverleaf tRNA secondary structure diagram. A percentage of modified nucleosides at each position is displayed as a pie chart at a corresponding position within the diagram.
3. Detailed data for a single position can be obtained by clicking at the given residue. The modification profile is then visualized as a pie chart in a separate panel, next to the cloverleaf graph.
4. Switching between three different ways of ordering the modification data within the pie chart is possible by using the "Sort by" options above the pie chart. By default, all types of modifications of one of the original unmodified nucleosides (A, U, C or G) follow that nucleoside in a pie chart (so modified ‘As’ are next to the unmodified ‘A’ etc.). Alternatively, all modified residues can be displayed next to each other. A chart with modified residues only can also be obtained
5. A summary of data for each position of the selected set of tRNA sequences can be also viewed as a table. The table is displayed after clicking at the icon located at the left side of the cloverleaf diagram. Positions in the tRNA are listed in rows and numbers of sequences that contain the particular nucleoside (modified or not) are presented in columns
6. To visualize the frequencies of A, U, C or G base occurrence (including both nascent and modified versions) in tRNA sequences use the "Draw AUCG profile" button at the sequence selection page. The results will be presented as four-color pie charts within cloverleaf diagram.