This is an exonerate fork with added gff3 support.
Original website with user guides: http://www.ebi.ac.uk/~guy/exonerate/
New Option: --gff3 [FALSE]
Using the "--gff3 yes" option with the "--showtargetgff yes" option will output GFF3. Without the "--gff3 yes" option, everything works just as before so previous scripts relying on the old output format won’t break.
Example Command:
exonerate -q protein.fa -t genome.fa --model protein2genome --querytype protein --targettype dna --showvulgar no --softmaskquery yes --softmasktarget yes --minintron 20 --maxintron 3000 --showalignment no --showtargetgff yes --showcigar no --geneseed 250 --score 250 --verbose 0 --gff3 yes
Example Output:
Scaffold1 exonerate:protein2genome:local match 188318 189587 649 - . ID=match00012;Name=EDAN000750-PA;Target=EDAN000750-PA 1 129 +;Gap=M135 D884 M251
Scaffold1 exonerate:protein2genome:local match_part 189452 189587 . - . Parent=match00012
Scaffold1 exonerate:protein2genome:local match_part 188318 188568 . - . Parent=match00012
Scaffold1 exonerate:protein2genome:local match 183667 183897 392 - . ID=match00013;Name=EDAN000750-PA;Target=EDAN000750-PA 127 203;Gap=M231
Scaffold1 exonerate:protein2genome:local match_part 183667 183897 . - . Parent=match00013
Scaffold1 exonerate:protein2genome:local match 45007 45165 265 - . ID=match00014;Name=EDAN000738-PA;Target=EDAN000738-PA 10 62;Gap=M159
Scaffold1 exonerate:protein2genome:local match_part 45007 45165 . - . Parent=match00014
Scaffold1 exonerate:protein2genome:local match 218654 221996 1577 + . ID=match00015;Name=EDAN000753-PA;Target=EDAN000753-PA 1 337 +;Gap=M30 D61 M100 D61 M127 D373 M181 D56 M225 D1183 M189 D604 M153
Scaffold1 exonerate:protein2genome:local match_part 218654 218685 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 218745 218846 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 218906 219034 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 219406 219586 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 219643 219867 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 221051 221239 . + . Parent=match00015
Scaffold1 exonerate:protein2genome:local match_part 221844 221996 . + . Parent=match00015