**What it does**

This tool finally runs the trained gene predictor, using the
genome-wide signal and content predictions, to predict genes on the
provided genomic sequence.  To this end, it computes a segmentation of
the sequence such that the segment types optimally agree with the
predicted contents and the segment boundaries optimally match the
predicted signals.

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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 be analyzed 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.
