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configurations.md

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SAUZEROR configurations

Flavour of SAUZEROR as file prefix

number what’s different
_ normal branch
3 alignment refinement
4 more PCs
6 LRs instead
7 3+4
9 3+6

Distance matrix

  • euclidean –> scipy.spatial.distance_matrix

  • normal distribution, CDF –> scipy.special.ndtr

ER/LR profiles

  • different amounts of principal components –> change indices of princo

  • different cutoffs; now always 5 Å - 14 Å as it's proven to be more performant

  • z-scaling of LRs before/after –> scale2 (from R, different to scipy.stats.scale)

Alignment/SW algorithm

  • gap and limit parameters
    –> [0-9]npanalysis.py for analysis of optimal new parameters

  • refinement step

Parameters in Smith-Waterman-algorithm for different profiles

description gap limit
normal ER, 1st PC of scaled or unscaled LRs 0.8 0.7
0.5 1.4
ER with 1st and 2nd PC 0.8 2.0
scaled LR 2.2 4.2
refinement step 0.4 0.2