Output format


DESCRIPTION

The output conforms to the GFF format. For each input sequence the server prints a list of predicted genes, one per line. The columns are: Only the predictions with R-values lower than the selected R-value cutoff (the default is 2) are reported.

The example below shows the EasyGene 1.2 output for the sequence taken from the GenBank entry AB010576, containing Bacillus subtilis ComX, ComQ and DegQ genes. All the three genes are predicted as annotated in the database (shown in green), with high confidence, although an alternative translation start is preferred for comQ (shown in orange). Two additional genes not annotated in the GenBank entry are also predicted.

EXAMPLE OUTPUT


##gff-version 2
##source-version easygene-1.2b
##date 2007-08-15
##Type DNA
# model:  BS03 Bacillus subtilis
# seqname       model   feature start   end       score        +/-      ?       startc  odds
# ---------------------------------------------------------------------------------------------
AB010576        BS03    CDS     67      324     0.0271875       +       0       #ATG    20.1861
AB010576        BS03    CDSsub  55      324     0.031955        +       0       #ATG    20.1731
AB010576        BS03    CDS     1129    1269    0.0190622       +       0       #ATG    15.7102
AB010576        BS03    CDS     1370    2314    2.13273e-12     +       0       #ATG    74.7815
AB010576        BS03    CDSsub  1454    2314    1.92405e-12     +       0       #ATG    74.6356
AB010576        BS03    CDS     2327    2491    0.0167943       +       0       #ATG    17.2951
AB010576        BS03    CDS     300     668     1.43511         -       0       #ATG    10.6215
# ---------------------------------------------------------------------------------------------