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Documents source of the "DNA1" score matrix from Travis.

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cryptogenomicon committed Aug 22, 2017
1 parent 337448f commit 41d7e9fe0f5913d66e14da4ab7cc323cbbe67406
Showing with 24 additions and 0 deletions.
  1. +24 −0 esl_scorematrix.c
@@ -735,6 +735,30 @@ struct esl_scorematrix_nt_preload_s {
int matrix[eslNTDIM][eslNTDIM];
};

/* "DNA1" matrix
*
* Travis Wheeler created the "DNA1" custom matrix for nhmmer. It's
* derived from the DNA prior (see <p7_prior_CreateNucleic()>), by
* computing mean posterior joint probabilities p_ij for a single
* observed count of each residue, assuming uniform background, and
* symmetricizing the result by taking means; then calling
* <esl_scorematrix_SetFromProbs()> with lambda = 0.02.
*
* The p_ij matrix was:
* A C G T
* 0.143 0.033 0.037 0.037 A
* 0.033 0.136 0.029 0.044 C
* 0.037 0.029 0.157 0.034 G
* 0.037 0.044 0.034 0.136 T
*
* Travis estimated the DNA prior from a subset of Rfam 10.0 seed
* alignments, based on a procedure from Eric Nawrocki: remove
* columns with >50% gaps, collect weighted counts, and estimate
* a four-component Dirichlet mixture.
*
* [xref email from Travis 8/21/2017]
*
*/
static const struct esl_scorematrix_nt_preload_s ESL_SCOREMATRIX_NT_PRELOADS[] = {
{ "DNA1", {
/* A C G T - R Y M K S W H B V D N * ~ */

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