Bradford Condon PhD

Bioinformatics, Web & Mobile Development


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.7

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

The 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)