minw and maxw parameters in psp-gen

[srivast...@gmail.com]

Do the -minw and -maxw values given as parameters in psp-gen and it's corresponding output given as input in MEME should be same? In the online version of MEME, for the -maxw values above 20 in psp-gen still gets input as 20. For example, for the motif width 6 to 50, on running MEME online and seeing the commands given as input, we find -minw value as 6 but -maxw for psp-gen to be equal to 20 whereas for motif width 7, both -minw and -maxw input in psp-gen is 7. Is it some error or something else? Kindly explain.  Thanks in advance :)

[James Johnson]

The reason we constrain the maximum width psp-gen tries to 20 is because larger values would just waste CPU cycles with no improvement.

The output PSP will have picked a word size between the minimum and maximum width that it considers ideal however it is exceedingly unlikely that this value would be 20 or larger even if you set the maximum width to allow it.

When MEME searches for a motif of a width that does not match the PSP it will copy and rescale the PSP to match that width using a geometric mean.