Generalize Needleman-Wunsch alignment #16
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The initial application of NW alignment was to find TM anchors. In that case, one is aligning a "probe" structure to 14 specific "reference residues," and thus the problem is quite asymmetric. There are applications where we would rather do "symmetric" alignment. This is basically a complete rewrite of the NW alignment code to allow for this. With the centroid/sidechain distance-based penalty, recommended gapcosts are: 5Å for extend, 20Å for open. These approximately maximize the agreement with the MSA pairings.
tmcgrath325
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May 17, 2024
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| # Saturating arithmetic to prevent overflow of Integer types | ||
| # https://discourse.julialang.org/t/the-performance-of-saturating-operations-or-adding-intrinsics/48575 | ||
| # (thanks!) | ||
| saturating_add2(x::T, y::T) where {T <: Unsigned} = x + min(~x, y) |
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Thanks for including the link! This is something I often forget about, since we often work with floats
tmcgrath325
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May 17, 2024
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The initial application of NW alignment was to find TM anchors. In that
case, one is aligning a "probe" structure to 14 specific "reference
residues," and thus the problem is quite asymmetric. There are
applications where we would rather do "symmetric" alignment. This is
basically a complete rewrite of the NW alignment code to allow for this.
With the centroid/sidechain distance-based penalty, recommended gapcosts
are: 5Å for extend, 20Å for open. These approximately maximize the
agreement with the MSA pairings.