rna2meme [options] <sequence file>
Convert an RNA sequence to its binding motif in MEME motif format.
A file containing short FASTA formatted
RNA sequences. If the file name is '-' then the file is read from standard input.
Writes MEME motif format to standard output.
A probability matrix and optionally a log-odds matrix are output for each motif in the file. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -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 |
| -bg | background file | The background file should be a Markov background model. It contains the background frequencies of letters use for assigning pseudocounts. The background frequencies will be included in the resulting MEME file. | Uses uniform background frequencies. |
| -pseudo | total pseudocounts | Add total pseudocounts times letter background to each frequency. | No pseudocount is added. |
| -logodds | Include a log-odds matrix in the output. This is not required for versions of the MEME Suite ≥ 4.7.0. | The log-odds matrix is not included in the output. | |
| -url | website | The provided website URL will be stored with the motif and this can be used by MEME Suite programs to provide a direct link to that information in their output. If website contains the keyword MOTIF_NAME the FASTA ID is substituted in place of MOTIF_NAME in the output. For example if the url is http://big-box-of-motifs.com/motifs/MOTIF_NAME.html and the FASTA ID is fasta_id, the motif will contain a link to http://big-box-of-motifs.com/motifs/fasta_id.html | The output does not include a URL with the motifs. |