Standard (Mandatory) qualifiers |
Allowed values |
Default |
[-sequence] (Parameter 1) |
Sequence database USA |
Readable sequence(s) |
Required |
-model |
Model to use |
oops | (Oops Distribution) | zoops | (Zoops Distribution) | tcm | (TCM Distribution) |
|
zoops |
-nmotifs |
Maximum number of motifs to find |
Any integer value |
1 |
[-outfile] (Parameter 2) |
Output file name |
Output file |
<sequence>.meme |
Additional (Optional) qualifiers |
Allowed values |
Default |
-ntype |
Method to use |
pair | (Pairwise method) | blend | (Blending method) |
|
pair |
-protein |
Assume sequences are proteins |
Boolean value Yes/No |
No |
-nucleic |
Assume sequences are DNA |
Boolean value Yes/No |
No |
-palindromes |
Allow palindromes |
Boolean value Yes/No |
No |
-ponly |
Force palindromes |
Boolean value Yes/No |
No |
-[no]shorten |
Allow motifs shorter than MINW |
Boolean value Yes/No |
Yes |
-nsites |
Expected number of sites for each motif |
Any numeric value |
0. |
-minsites |
Minimum number of sites for each motif |
Any numeric value |
0. |
-maxsites |
Maximum number of sites for each motif |
Any numeric value |
0. |
-w |
Starting motif width to try |
Any integer value |
0 |
-minw |
Minimum starting motif width to try |
Any integer value |
8 |
-maxw |
Maximum starting motif width to try |
Any integer value |
57 |
-prior |
Prior to use |
dirichlet | (Dirichlet prior) | dmix | (dmix prior) | mega | (mega prior) | megap | (megap prior) | addone | (addone prior) |
|
dirichlet |
-[no]brief |
Don't print documemtation |
Boolean value Yes/No |
Yes |
-b |
Strength of the prior |
Any numeric value |
-1.0 |
-spmap |
Mapping start |
uni | (uni map type) | pam | (pam map type) |
|
uni |
-spfuzz |
Fuzziness of sequence to theta mapping |
Any numeric value |
-1.0 |
-maxiter |
Maximum EM iterations to run |
Any integer value |
50 |
-distance |
EM convergence criterion |
Any numeric value |
1e-3 |
-cons |
Consensus sequence to start EM from |
Any string is accepted |
An empty string is accepted |
-chi |
Cutoff for p-value |
Any numeric value |
1.0 |
-adj |
Type |
none | (no LRT) | bon | (bon LRT) | root | (root LRT) |
|
root |
-maxsize |
Maximum dataset size in characters |
Any integer value |
100000 |
-page |
Width of page |
Any integer value |
80 |
-status |
Print progress reports |
Boolean value Yes/No |
No |
-v |
Verbose mode |
Boolean value Yes/No |
No |
-cfive |
Use 5' to 3' complementary strand as well |
Boolean value Yes/No |
No |
-cthree |
Use 3' to 5' complementary strand as well |
Boolean value Yes/No |
No |
-wthree |
Use 3' to 5' main strand as well |
Boolean value Yes/No |
No |
-prob |
Starting point confidence level |
Any numeric value |
1.0 |
-seed |
Seed for random numbers in sampling |
Any integer value |
0 |
-seqfrac |
Fraction of sequences to use |
Any numeric value |
1.0 |
-[no]align |
Print aligned motif occurrences |
Boolean value Yes/No |
Yes |
-trace |
Trace starting points |
Boolean value Yes/No |
No |
-allprint |
Print all debugging information |
Boolean value Yes/No |
No |
-wprint |
Print erasure matrix |
Boolean value Yes/No |
No |
-zprint |
Print missing information matrix |
Boolean value Yes/No |
No |
-llprint |
Print log likelihood during EM |
Boolean value Yes/No |
No |
-startsprint |
Print starting points |
Boolean value Yes/No |
No |
-fastaprint |
Print sites in FASTA format |
Boolean value Yes/No |
No |
-timer |
Timer type |
Any integer value |
0 |
Advanced (Unprompted) qualifiers |
Allowed values |
Default |
(none) |
Program name | Description |
antigenic | Finds antigenic sites in proteins |
digest | Protein proteolytic enzyme or reagent cleavage digest |
epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
pepcoil | Predicts coiled coil regions |
preg | Regular expression search of a protein sequence |
pscan | Scans proteins using PRINTS |
sigcleave | Reports protein signal cleavage sites |