Comments on RRResearch: The postdoc's new analysis saves us work

I have also preferred the final possibility (the i...

2011-12-29T13:07:58.883-08:00

I have also preferred the final possibility (the interactions explain the discrepancy). But we can't entirely discount the other two without some other work.

I think the use of "complex" above is confusing. Sequences with high scores using the genomic motif have LESS potential complexity than sequences with high scores using the uptake motif. More "specific" or more "informative" might make more sense.

"This is done with each strand of the 1,830,1...

2011-12-29T12:59:54.908-08:00

"This is done with each strand of the 1,830,138 bp genome, so a total of 3,660,276 scores are generated with each motif."

As a side-note, since the scoring matrix is 32 positions long, There are only 1,830,107 alignment frames for a linear sequence. To get all frames, I pseudo-circularized the genome by duplicating the first 31 bases of the genome and concatenating them to the end.