A tab must separate each column in the gff file.
## Denotes comment lines and are ignored by GATA.
Follow the examples.
|Chromosome/SeqName||Only used by GATA as name for the feature when a "name=value;" attribute is missing. Otherwise it is ignored.|
|Source||Not used by GATA.|
Recognized features are incorporated into gene group annotation and drawn as a unit, independent of other gene groups. These gene groups typically contain one or more transgroups/splice forms (exons/ translation /transcription) and a gene (DNA). Recognized features include: "exon", "transcript", "translation", "*gene*", "*rna*", "*transpos*", "*misc*". Where an "*" represents one or more wildcards. For example GATA will recognize "trna", "snRNA", "rRNA", "misc. non-coding RNA", etc. Case insensitive. The order of elements within a gene group is important. List exons first, then one translation (if present), then one transcript. Do this for each transgroup and finally list the closing feature, typically just a "gene" or "*rna*", "*transpos*", "*misc*". Follow the examples.|
Features not recognized by GATA are assigned to individual tracks. The Feature column is a good place to put hits to transcription factor binding motifs (e.g. "HunchBack") or cis regulatory modules (e.g. CRM). Use this feature column for putting in a generic name, not a specific name (e.g. bad -> CRM1, CRM27, etc) since each unrecognized feature will be assigned a separate track.
|Start||Where a feature starts, an integer (e.g. given gggggATGCATTAGccccc, the translation would start at A, base 6). Start is always less than End.|
|End||Where the feature ends, an integer, inclusive (e.g. the translation above would end on G, base 14). End is always greater than Start.|
|Score||This number is not used in painting recognized features like exons, but can be used to shade unrecognized feature tracks such as hits to transcription factor binding motifs.|
|Strand||Used to orientate the arrows associated with annotation features where "+" denotes left to right, "-" right to left.|
|Frame||Not used by GATA.|
|Attributes/ Comments||Must contain at least one "key=value; " pair. This is a good place to put a unique identifier like "name=CG12445;" or "name=HunchBack hit 27;". If present, the name=value will be extracted by GATA and displayed as the features label. A ";" should be used to close the value parameter.|