Specify a file to upload containing sequence coordinates in BED format. The file must be based on the exact genome version you specified in the menus above.
Select an available sequence database from this menu.
Select an available version of the sequence database from this menu.
Select an available tissue/cell-specificity from this menu.
Selecting this option will filter the sequence menu to only contain databases that have additional information that is specific to a tissue or cell line.
This option causes MEME Suite to use tissue/cell-specific information (typically from DNase I or histone modification ChIP-seq data) encoded as a position specific prior that has been created by the MEME Suite create-priors utility. You can see a description of the sequence databases for which we provide tissue/cell-specific priors here.
Note that you cannot upload or type in your own sequences when tissue/cell-specific scanning is selected.
Enter text naming or describing this analysis. The job description will be included in the notification email you receive and in the job output.
This is the width (number of characters in the sequence pattern) of a single motif. STREME chooses the optimal width of each motif individually using a heuristic function. You can choose limits for the minimum and maximum motif widths that STREME will consider. The width of each motif that STREME reports will lie within the limits you choose.
If you do not specify a set of control sequences, STREME will create one by shuffling each primary sequences while preserving the frequencies of all words of length order+1 that it contains. STREME also creates a Markov model of the given order from the control sequences that you provide, or from the shuffled primary sequences. Check this box and set the value of order if you want to override the default value that STREME uses.
When your sequences are in the DNA alphabet but you want them to be treated as single-stranded RNA, check this box.