rna2meme [options] <sequence file>
Convert each RNA sequence in the input to a DNA motif in MEME motif format.
The name of a file containing short FASTA formatted
RNA sequences. If the file name is '
-' then the file is read from standard input.
|-rna||Output RNA motifs instead of DNA motifs.||Output DNA motifs.|
|-seed_start||offset||The starting offset of the seed in the (micro-)RNA sequence. If this value is 0, the entire sequence is treated as the seed (see -other_count below).||0: the entire RNA sequence is treated as the seed.|
|-seed_end||offset||The ending offset of the seed in the (micro-)RNA sequence. This option is ignored if -seed_start is 0.||0|
|-start||offset||The starting offset in the RNA sequence (inclusive). Use negative numbers to count from the end. Do not use this option in conjunction with -seed_start.||No starting offset is used.|
|-end||offset||The ending offset in RNA sequence (inclusive). Use negative numbers to count from end. Do not use this option in conjunction with -seed_start.||No ending offset is used.|
|-match||count||The count to assign to a match (complement).||A count of 1 is used.|
|-wobble||count||The count to assign to a U for a G, or a G for a U.||A count of 0.1 is used.|
|-miss||count||The count to assign to a non-match non-wobble.||A count of 0.01 is used.|
|-other_count||count||Extra count to add to match, wobble and misses in the non-seed regions. Setting this to a large value reduces the effect of poor matching in the non-seed regions; setting this to zero causes seed and non-seed regions to be weighted equally.||0.5|