EMBOSS explorer


Motif detection (read the manual)

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

Input section
MEME program output file:
FASTA-formatted sequence file:
Sequence file is a list of fasta-formatted databases?
MEME background frequencies file (optional):
Required section
Print results for sequences with E-value
Show motif matches with p-value < mt
Additional section
Read database from standard input?
Output in text (ASCII) format?
Output in hypertext (HTML) format?
Translate DNA sequences to protein?
Adjust p-values and E-values for sequence composition?
Include only the best motif in diagrams?
Remove highly correlated motifs from query?
Do not print progress report?
Advanced section
Only use the first <c> motifs
Score reverse complement DNA strand as a separate sequence?
Do not score reverse complement DNA strand?
Show weak matches (mt<p-value<mt*10) in angle brackets?
Use SEQUENCE p-values for motif thresholds?
Print <mf> as motif file name.
Print <df> as database name.
Print <dl> as link to search sequence names.
Lower bound on number of sequences in db
Use only motifs with E-values less than <mev>
Use only motif(s) number <m>
Nominal order and spacing of motifs
Output section
Overwrite files in the output directory?
Print hit_list instead of diagram; implies -text?
Run section
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