
Michael E Sparks
5 August 2007

(All included binary files were generated on a little-endian system.)

0README -- this file

Ptrich.exonct -- Exon count distribution as learned from a spliced
  alignment dataset of 89,943 Populus trichocarpa EST sequences against the
  19 assembled linkage groups, available in GenBank as of 2 February 2007,
  using version 1.0.0 of the GenomeThreader package.

Ptrich.bssm -- Parameters for a splice site WAM, learned from the
  aforementioned GenomeThreader alignment dataset using the BSSM4PASIF
  package.

Ptrich.CHI2, Ptrich.DMMM, Ptrich.FIXORD -- Markov chains learned from a
  cleaned version of the Populus trichocarpa v1.1 ``Jamboree'' annotations.

Ptrich.genconf -- General configuration settings for PASIF.  Please read the
  commentary in the file for details.

Ptrich.linunit -- Parameters for a trained linear unit.
  Error converged to an approximate minimum (595.133793) after 10000
  iterations over the dataset.
  (Note that ``error'' refers to mean square error.)

Ptrich.sigunit -- Parameters for a trained sigmoidal unit.
  Error converged to an approximate minimum (61.849861) after 25000
  iterations over the dataset.
  (Note that ``error'' refers to mean square error.)

