
 Files in the 'proben1/gene' directory:
========================================

This dataset is from the UCI machine learning database:
"splice-junction gene sequences"

[Remark: some of the generated files may not exist in order to save disk space]

splice.names
  Original documentation for the dataset

splice.data
  Original data file

splice.theory
  Domain theory for the dataset:
   "If exact matches are required, then this set of rules correctly identifies 
    40% of the IE examples, 4% of the EI examples and 99% of the neither
    examples. 48 examples are falsely classed as IE. No examples are falsely
    classed as EI."

gene.cod
  train.num encoded in the way described in the 'design' section below

header
  Header lines used in .dt files

gene?.dt
  different permutations of the lines of gene.cod plus the header lines

raw2cod
  Perl script for format conversions:
  takes gene.data as input and produces gene.cod as output according
  to the rules given in section 'design' below.

Makefile
  Makefile to call scripts to create .dt  files

 
 Encoding:
===========

Output: The output encoding is a simple 1-of-3 encoding as follows:
          EI  1 0 0
          IE  0 1 0
          N   0 0 1        
Input:  Each nucleotide in the gene sequence window is represented by
        a pair of inputs, using the following binary encoding:
          C   -1  -1
          A   -1   1
          G    1  -1
          T    1   1
        This results in having 120 inputs to the network.


Remarks:
  a few lines in the file had one or several nucleotid codes 'N' in the
  sequence window, meaning unknown nucleotids.
  These have been filtered out.
  The previous result file gene.cod had lines with
       1 x length  125 (368-125 = number of 'N' nucleotides)
       1 x length  353
       3 x length  359
      10 x length  365
    3175 x length  368
  Now the illegal shorter lines have been left out.

