elm2meme [options] <ELM file>+
Reads a tab separated quoted values file containing ELM regular expressions and convert them to MEME motifs where possible.
Reads ELM entries from the listed files.
ELM entries describe a motif as a regular expression. Not all can be converted into MEME motifs due to anchors or variable length.
"Accession" "ELMIdentifier" "FunctionalSiteName" "Description" "Regex" "Probability" "#Instances" "#Instances_in_PDB"
"ELME000321" "CLV_C14_Caspase3-7" "Caspase cleavage motif" "Caspase-3 and Caspase-7 cleavage site." "[DSTE][^P][^DEWHFYC]D[GSAN]" "0.00309374033071" "39" "0"
"ELME000172" "CLV_MEL_PAP_1" "Melanisation activation site" "Prophenoloxidase-activating proteinase (PAP) cleavage site ([ILV]-X-X-R-|-[FV]-[GS]-X)." "[ILV]..R[VF][GS]." "0.000105375572148" "12" "0"
"ELME000102" "CLV_NRD_NRD_1" "NRD cleavage site" "N-Arg dibasic convertase (NRD/Nardilysin) cleavage site (X-|-R-K or R-|-R-X)." "(.RK)|(RR[^KR])" "0.00746473248158" "2" "0"
"ELME000101" "CLV_PCSK_FUR_1" "PCSK cleavage site" "Furin (PACE) cleavage site (R-X-[RK]-R-|-X)." "R.[RK]R." "0.000508722921034" "13" "0"
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 | |||
| -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 motif 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 motif ID is NANOG, the motif will contain a link to http://big-box-of-motifs.com/motifs/NANOG.html | The output does not include a URL with the motifs. |
| -h | Prints a usage message and exits. | The program runs as normal. | |