Mercurial > repos > iuc > funannotate_annotate
diff test-data/funannotate_db/trained_species/fly/augustus/fly_weightmatrix.txt @ 0:a5baa4ff168d draft
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
author | iuc |
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date | Mon, 04 Oct 2021 19:39:38 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/trained_species/fly/augustus/fly_weightmatrix.txt Mon Oct 04 19:39:38 2021 +0000 @@ -0,0 +1,23 @@ +# +# This file contains a matrix used for weighing the training sequences +# when given an input sequence. Let z = (da, dc, dg, dt) be the vector +# containing the differences in the relative nucleotide frequencies of +# two sequences, the input sequence and a training sequence. +# Then the training sequence has weight proportional to +# +# exp ( - z M z^t) +# +# with M being the matrix specified below. +# If M is nonsingular, then (apart from a two normalizing factors) M +# is the inverse of the covariance matrix of a multinormal +# distribution - the kernel for the estimation. + + +# this matrix is gc-content only, i.e. +# weight = 10 * exp (-200 * (dc + dg))^2) +# in particular weight <= 10 +0 0 0 0 +0 200 0 0 +0 0 200 0 +0 0 0 0 +