Ian Korf’s Zoe File Format. It looks a lot like GFF but has a > header which defines the name of the sequence and lacks the seq_id column accordingly.
The following is from the SNAP documenation about ZFF:
What is ZFF? It is a non-standard format (ie. nobody uses it but me) that bears resemblance to FASTA and GFF (both true standards). ZFF is also the input format for training data to SNAP making it very easy to train SNAP on new genomes.
There are two styles of ZFF, the short format and the long format. In both cases, the sequence records are separated by a definition line, just like FASTA.
In the short format, there are 4 fields: Label, Begin, End, Group. The 4th field is optional. Label is a controlled vocabulary (see zoeFeature.h for a complete list). All exons of a gene (or more appropriately a transcriptional unit) must share the same unique group name. The strand of the feature is implied in the coordinates, so if Begin > End, the feature is on the minus strand. Here’s and example of the short format with two sequences, each containing a single gene on the plus strand:
>sequence-1
Einit 201 325 Y73E7A.6
Eterm 2175 2319 Y73E7A.6
>sequence-2
Einit 201 462 Y73E7A.7
Exon 1803 2031 Y73E7A.7
Exon 2929 3031 Y73E7A.7
Exon 3467 3624 Y73E7A.7
Exon 4185 4406 Y73E7A.7
Eterm 5103 5280 Y73E7A.7
The long format adds 5 fields between the coordinates and the group: Strand, Score, 5’-overhang, 3’-overhang, and Frame. Strand is +/-. Score is any floating point value. 5’- and 3’-overhang are the number of bp of an incomplete codon at each end of an exon. Frame is the reading frame (0..2 and not 1..3). Here’s an example of the long format:
>Y73E7A.6
Einit 201 325 + 90 0 2 1 Y73E7A.6
Eterm 2175 2319 + 295 1 0 2 Y73E7A.6
>Y73E7A.7
Einit 201 462 + 263 0 1 1 Y73E7A.7
Exon 1803 2031 + 379 2 2 0 Y73E7A.7
Exon 2929 3031 + 236 1 0 0 Y73E7A.7
Exon 3467 3624 + 152 0 2 0 Y73E7A.7
Exon 4185 4406 + 225 1 2 2 Y73E7A.7
Eterm 5103 5280 + 46 1 0 2 Y73E7A.7"