ZFF annotations for SNAP
This post is part 6 of a series on file formats, written for the 2017 UK-KBRIN Essentials of Next Generation Sequencing Workshop at the University of Kentucky.
SNAP and ZFF
SNAP stands for Semi-HMM-based Nucleic Acid Parser, it is a general purpose gene-finding utility.
The ZFF file is generated with maker2zff and is fed into the fathom command
To read more, read the README file distributed with SNAP. Examples are taken from https://crc.ibest.uidaho.edu/help/Applications/SNAP.html.
ZFF format
Gene structure files are in ZFFformat. Confusingly, this is the file with the .ann extension. It is a non-standard file format that resembles both FASTA and GFF. There is both a short and long format.
Short format
>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.7Long 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.7The below table describes each column
| ID | Type | Description |
|---|---|---|
| Label | Short | See zoeFeature.h for a complete list of possible values |
| Begin | Short | Start location |
| End | Short | End location |
| Group | Short (optional) | All exons must share a group name |
| Strand | Long | Plus or minus strand |
| Score | Long | A float type integer for score. This score depends on the method used to generate the file. |
| 5'-overhang | Long | Number of bp of incomplete codon 5' |
| 3'-overhang | Long | Number of bp of incomplete codon 3' |
| Frame | Long | Reading frame (0, 1, 2) |