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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 29 30 31 32 33 34 35 36 37 | ##gff-version 3
#
#Alignments
#
#Nucleotide to genome, and protein to genome alignments are a little
#tricky because they involve two coordinate systems, the coordinates
#of the alignment on the genome (known as the "source" coordinates),
#and the coordinates of the cDNA, EST or protein (known as the
#"target" coordinates). In GFF3, the target coordinates are specified
#using the Target tag.
#This example shows three different alignment features of type
#"EST_match". Each alignment has a distinct ID, and all the
#discontinuous parts of the alignment have the same ID, as described
#earlier. In addition to the ID and Name tags, each segment also has a
#Target tag whose value has the format "<target seqid> <target start>
#<target end>." For example, the very first line indicates that the
#EST named agt830.5 aligns to genomic contig ctg123 such that
#positions 1 through 451 of agt830.5 aligns to bases 1050-1500 of
#ctg123.
#Using the ##FASTA section of the GFF3 file, you can specify the
#sequence of the ESTs as well as of the contig, and GBrowse will
#display the DNA and/or protein sequences in the appropriate contexts.
#See the GFF3 specification for instructions on how to represent
#gapped alignments.
ctg123 est EST_match 1050 1500 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 451
ctg123 est EST_match 3000 3202 . + . ID=Match1;Name=agt830.5;Target=agt830.5 452 654
ctg123 est EST_match 5410 5500 . - . ID=Match2;Name=agt830.3;Target=agt830.3 505 595
ctg123 est EST_match 7000 7503 . - . ID=Match2;Name=agt830.3;Target=agt830.3 1 504
ctg123 est EST_match 1050 1500 . + . ID=Match3;Name=agt221.5;Target=agt221.5 1 451
ctg123 est EST_match 5000 5500 . + . ID=Match3;Name=agt221.5;Target=agt221.5 452 952
ctg123 est EST_match 7000 7300 . + . ID=Match3;Name=agt221.5;Target=agt221.5 953 1253
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