User:ElNando888/WikiGetSat/Ideas/Sequences sorting in labs
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Bottom-level, the discussion.
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One beautiful feature would be the possibility to wikify those contents.
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If I'm not mistaken, sequences in labs can be sorted, and the algorithm currently in use seems to be the Hamming distance.
I'd like to propose a new sorting algorithm (which I dubbed “LDq9”), based on a Lee distance metric with a pseudo-alphabet of size 9 (or more). An example mapping would be:
A.G.-.-.U.C.-.-.-
0.1.2.3.4.5.6.7.8
Which would result in following specific distances:
A:G = 1
U:C = 1
G:C = 4
G:U = 3
A:U = 4
A:C = 4
The basic idea simply being that, changes within the same nucleotide classes (purines or pyrimidines) represent a short distance, while a change of class represent a larger jump.
I believe that this would give a somewhat better view of the similarity of sequences, specially in the context of switches.
-- ElNando888
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Nice Idea.
-- jandersonlee
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Hmm. Suppose I change a GC bond to CG. How does that get scored? And should it differ if it's a switch lab or not?
-- jandersonlee
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GC to CG would be a +8 step.
I don't think the metric should change between static labs and switch ones, but this idea of mine may prove making little difference with a simple Hamming in the case of static target structures.
For switches, I'm almost convinced that this sorting would be a lot more accurate.
-- ElNando888
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Worth a try if the coding isn't too much.
-- eternacac
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