Hairpin barcode skews up comparison of designs

Iroppy came up with a great idea that will help us better compare designs when looking at the lab results. Count only GC-pairs from main design, not the hairpin barcode. The GC-pairs in the hairpin can totally skew GC-pair percentage for designs and make comparison harder.

lroppy: lab idea [5:13 PM]

Eli Fisker: yes, let me hear [5:14 PM]

lroppy: When we publish lab results [5:14 PM]

lroppy: and maybe submittals too [5:14 PM]

lroppy: we should publish the statistics for # of bonds as adjusted for the bar code [5:14 PM]

lroppy: stack [5:14 PM]

lroppy: because [5:14 PM]

lroppy: it is not intended to be part of the [5:15 PM]

lroppy: design [5:15 PM]

lroppy: just an artefact of the process [5:15 PM]

lroppy: if you look at a GC count for synth designs [5:15 PM]

Eli Fisker: do you mean sort of statistics of how good individual barcodes are, so people can avoid the worst ones? [5:15 PM]

lroppy: they are all distorted [5:15 PM]

lroppy: no [5:15 PM]

Eli Fisker: ah [5:15 PM]

lroppy: altho the general question of whether we are marked down if we are forced to use a poor barcode is relevant as well, but separable [5:16 PM]

lroppy: for my idea [5:16 PM]

Eli Fisker: I very much agree with your observation. Makes it harder to judge lab designs from the lab results, when looking at GC-pairs % which is part of what I do [5:16 PM]

lroppy: assume that all bar codes synthesize [5:16 PM]

lroppy: properlyt [5:16 PM]

lroppy: yes [5:16 PM]

lroppy: exacly [5:16 PM]

lroppy: I just reviewed my own submittal on 9 [5:16 PM]

lroppy: and thought my GC were way too high [5:17 PM]

lroppy: but it was just the barcode I had selected [5:17 PM]

lroppy: and realized same prob when you see results [5:17 PM]

Eli Fisker: Yes. also the barcode affect how the melt plot appears [5:17 PM]

lroppy: so for labs, it should show adjusted #s [5:17 PM]

Eli Fisker: you can mask a bad melt plot by GC-ing out the barcode [5:17 PM]

lroppy: true. but easy to adjust for it in the # of bonds [5:17 PM]

Eli Fisker: agree [5:18 PM]

lroppy: would be goods to do as well [5:18 PM]

lroppy: anyway [5:18 PM]

lroppy: EOI [5:18 PM]

Eli Fisker: I like your idea very much. I think you should suggest it in the forum [5:18 PM]

lroppy: end of idea [5:18 PM]

Hmm. GC pairs in the hairpin can interact with the rest of the design and cause misfolds elsewhere. My hunch is to leave them in the count.

I always compare the “design” by using identical hairpins ( a real hassle), because, yes it does interact on dot plot, melt temp, and total reported energy, and probably real lab folding too.

Except for when I’m lazy :slight_smile:

Agree, hairpins can interact and mispair with the rest of the design. So true they should propably stay in count. But I don’t like that they interfere with my usual “statistics” on percentage of basepairs in a design. Because the % do tell me something about how likely a design is to succede with a given amount of GC-pairs. Depending on the structure of the design. (longstringed or pressured) And the hairpin interfere with that and makes the picture a bit more muddy. Thx for your concern.