Hi. I just got done running R100 through DPAT and here is all the data it generated through the macro search filter settings for 80-100 scores and 30 60 group scores designs for everyone to use. There are 3 types of files for each single oligo sublab group of 80-100 and 30 60 groups. There is the file with just the round number and sublab name which has just the list of markers from the MFE secondary structure.There is a RawDesignInfo file that has all the unique secondary structures that fit the search criteria along with sequences and partition function information when available. There is also a Report file that has a bunch of things going on.
The report file starts with a summary of the structural characteristics of the results of the macro search. It has the averages of stacks and pairs for the whole set of results and the standard deviations of the averages. This is broken into two two groups that repeat. The two groups are designs that have stacks that have stacks that fit the search criteria as well as stacks that don’t fit the search criteria (which is the first group) and the designs that have all stacks that fit the search criteria (the second one). Then there is a list of each unique secondary structure and the number of times it appears in the search criteria as well as the number of pairs and stacks and ratios. I was doing some research into this before I changed focus and worked on how to detect the 30 60 group. This data is repeated again but for the second group as described above and at the very end is a list of all the stacks found that fit the search criteria.
Also included are the raw DPAT data files with all the stacks and the pairing probabilities for the stacks that were used as a source for the searches.
The DPAT data I used as the constraints for Sara in R101 is the plain names file for the markers, the partition function data ranges for the applicable score group, and the pairing probabilities of “ideal” binding sites which don’t exist for these sublabs. So I would recommend designing for round 2 of R100 so that at least one of the stacks in the 80-100 score group is in your design for a good chance at a high scorer and that the partition function values are in the same range as the good results. I can have values for you tomorrow but I need to go to bed now.
I fixed the link and added more files and fixed my error in calling this round 101 vrs 100. I have included the macro settings file I used along with an explanation of DPAT’s language for a detailed explanation of what was searched. Basically DPAT looked at specific score ranges and picked out structures that were only present in those score ranges.