Analysis of NP-GG differences (I can't help myself!)

Despite my sensible conclusion to the previous post, I've rushed in with a bit of analysis of the reasons for the differences between the NP and GG uptake-ratio peaks.I was able to do this because the PhD student just posted two new graphs, showing the uptake peaks in syntenic 20 kb segments of the NP and GG genomes.The peaks for the two genomes are in the same places because the underlying DNA sequences are very similar.  Most of the peaks also have similar heights in the two genomes, with two obvious exceptions (labelled Discordant peak 1 and Discordant peak 2).  Here are those peaks side-by-side, to the same scale:To look for sequence differences that could explain these uptake differences, I copied the corresponding DNA sequences for these regions from Genbank and examined them for USS.  I easily found good matches to the USS motif at the centers of both peaks. Here are the GG and NP sequences for Peak 2, which has the bigger difference in height.  I've included a logo showing the USS-uptake motif we determined earlier.There are lots of differences over this 66 bp segment.  None are in the 9 bp USS core, but there are 4 base substitutions and a single-base deletion in the 'unimportant' parts of the motif, and 5 more substitutions nearby.  In principle any of these differences could be responsible for the uptake difference.But here are the corresponding sequences for Discordant peak 1.  (It's in the other orientation in the genome.)T...
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs