EMBOSS explorer


Multiple EM for motif elicitation (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Set of sequences (not a USA!). Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
MEME background Markov model file (optional):
MEME dirichlet prior file (optional):
Required section
Additional section
Select motif distribution
Maximum number of motifs to find
Output in text format (default is HTML)?
Prior to use
Threshold value of motif E-value at which to stop searching.
Number of sites for each motif
Minimum number of sites for each motif
Maximum number of sites for each motif
Weight on expected number of sites
Motif width
Minumum motif width
Maximum motif width
Do not adjust motif width using multiple alignment.?
Gap opening cost for multiple alignments
Gap extension cost for multiple alignments
Do not penalise end gaps in multiple alignments?
Allow sites on + or - DNA strands?
Look for palindromes (requires input sequence to be dna)?
Do not print progress reports to terminal?
Advanced section
Maximum EM iterations to run
EM convergence criterion
Strength of the prior
Fuzziness of sequence to theta mapping
Select type of mapping
Consensus sequence to start EM from
Maximum dataset size in characters (-1 = use meme default).
Use parallel version with <p> processors
Quit before <time> CPU seconds consumed
Print <sf> as name of sequence file
Maximum size of heap used during a branching search
Perform x-branching?
Perform width branching?
Number of iterations in the branching search
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.