/usr/share/EMBOSS/test/data/gmod-discontinuous.gff3 is in emboss-test 6.4.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ##gff-version 3
#
#Discontinuous Features
#
#In addition to nested features, another common type of genomic
#annotation is the discontinuous feature in which a single feature
#spans multiple discontinuous portions of the genome. The primary
#example is an alignment, such as a cDNA sequence that has been
#aligned to genomic sequence. GFF3 deals with these features by
#representing each continuous segment as a distinct row, and then
#giving each segment the same ID to tie them together. For example:
#
#Note that this is distinct from the nested features we looked at in
#the previous section. In the former case, there is a single parent
#feature and multiple child features that are linked to the parent via
#a Parent tag. The IDs of the children are distinct from each other
#(or absent altogether). In the latter case, each segment of the
#discontinuous feature has the same ID. There is no parent.
#
#Note that this method of grouping discontinuous features is not
#currently supported by the GMOD Chado bulk GFF3 loader. Parent-child
#grouping is required.
#
ctg123 example match 26122 26126 . + . ID=match001
ctg123 example match 26497 26869 . + . ID=match001
ctg123 example match 27201 27325 . + . ID=match001
ctg123 example match 27372 27433 . + . ID=match001
ctg123 example match 27565 27565 . + . ID=match001
|