Difference between revisions of "Template:GFF3FASTA"
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m (New page: GFF3 files can also include sequence in FASTA format at the end of the file. The FASTA sequences are preceded by a <tt>##FASTA</tt> line. This sequence section is optional. If presen...) |
(New page: GFF3 files can also include sequence in FASTA format at the end of the file. The FASTA sequences are preceded by a <tt>##FASTA</tt> line. This sequence section is optional. If presen...) |
(No difference)
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Revision as of 01:02, 8 March 2011
GFF3 files can also include sequence in FASTA format at the end of the file. The FASTA sequences are preceded by a ##FASTA line. This sequence section is optional. If present, the sequence section can define sequence for any landmark used in column 1 (the frame of reference). For example: For example:
##gff-version 3 ctg123 . exon 1300 1500 . + . ID=exon00001 ctg123 . exon 1050 1500 . + . ID=exon00002 ctg123 . exon 3000 3902 . + . ID=exon00003 ctg123 . exon 5000 5500 . + . ID=exon00004 ctg123 . exon 7000 9000 . + . ID=exon00005 ##FASTA >ctg123 cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc ...
When the GFF3 file is processed the IDs on the header line of FASTA entries are matched with IDs used in column 1 in the annotation section of the file.
You don't have to store the FASTA in the GFF file. You can also store your sequences in a separate file containing only FASTA entries.
