background model and discriminative search

[Devinder Kaur]

Hi,

As we generated a file using psp-gen for discriminative motif search, does we need to provide the following optional information while running meme:

-mod zoops
-minw
-maxw
-nmotif (does the mod, width and nmotif be estimated from psp-gen file automatically?)
specially do we need to provide the -bfile (background model)

or we can run meme like:

1) $ psp-gen -pos inputseq.fasta -neg neg-dna.fasta > dna.psp

2) $ meme -inputseq.fasta -psp dna.psp -oc meme_out -dna -mod zoops -minw 6 -maxw 16 -nmotifs 10 -bfile background.model -maxsize 6000000

Second, will the -minw for "selecting the "best" width for PSPs" and -minw for "Search for motifs with a width" be set to same integer value ?

[CharlesEGrant]

The purpose of psp-gen is to calculate the position-specific priors used by MEME in discriminative search. The calculate values of the priors are the only information in the output of psp-gen. It doesn’t contain any of the settings to be used by MEME. See the description of the PSP file format for more information.

So yes, you do need to provide the values for both the ‘meme’ and ‘psp-gen’ command line parameters, or they will be set to their default values. By default ‘meme’ will generate a 0th order background model from the input sequences. Depending on the circumstances of your experiment it may be worthwhile to use a higher-order model