A methylation file can be created for each target RNA sequence (i.e. rRNAs) to specify the positions that are known or expected to be 2'-O-ribose methylated. These sites are usually based on biochemical evidence, or inferred from related species with reliable methylation site data.
The basic format for a methylaiton file is
>Target-seq-name1 N Number "My comment"Where:
Multiple methylation sites for multiple sequences can be specified in one file, and do not need to appear in the same order as in the target sequence FASTA file (but the sequence names MUST match). Also, you do NOT need to supply methylation information for each target sequence, just those you have data for.
For example, if you submitted this FASTA target sequence to the server:
>My-seq-A small subunit ribosomal sequence from my favorite organism TATCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC ATGCATGTCTAAGTATAAGCAATTTATACAGTGAA >My-seq-B large subunit ribosomal sequence from my favorite organism GATGTATTTATTAGATAAAAAATCAATGTCTTCGGACTCTTTGThen the methylation file specifying sites in these target sequences might look like:
>My-seq-A T 5 Verified meth site by TML C 12 Predicted by snoscan A 51 Known target of U21 >My-seq-B G 1 Partially modified site A 6 Mapped by MadenSee the sample yeast and human methylation site files on the main search page for more examples.