**What it does**

This tool trains the integrative layer of mGene (layer 2).  Based on the
genome information file, the genome-wide predictions for all relevant
signals and a set of annotated genes (in GFF3 format), mGene learns to
predict gene structures on genomic DNA.

The training time may be roughly on the order of 3h times the number
of genes in the training set.

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**Output**

The output consistes of a set of predicted genes that is stored in a
file in GFF3 format.  It may typically be used with 'GenePredict'.
The training error may be evaluated with 'GeneEval'.

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**About formats**

**GFF format** General Feature Format is a format for describing genes
and other features associated with DNA, RNA and Protein sequences. GFF
lines have nine tab-separated fields::

    1. seqname - Must be a chromosome or scaffold.
    2. source - The program that generated this feature.
    3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
    4. start - The starting position of the feature in the sequence. The first base is numbered 1.
    5. end - The ending position of the feature (inclusive).
    6. score - A score between 0 and 1000. If there is no score value, enter ".".
    7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
    8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
    9. group - All lines with the same group are linked together into a single item.

**SPF format** Signal Prediction format was designed for providing
information such as labels or predictions for specific genomic locations
(with strand information). It has requires exactly six fields::

    1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
    2. signalName - possible choices include tss, tis, acc, don, cdsStop, cleave.
    3. scoreName - possible choices include label, output, Conf, Conf_Cum
    4. chromPos - The position in the chromosome. (The first base in a chromosome is numbered 1.)
    5. strand - Defines the strand - either '+' or '-'.
    6. score - The score between -infinity and infinity. If scoreName is 'label', then the score should be either -1 or 1.
