Dear Maker developper,
I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :
###
ctg889_racon_pilon3
tblastx translated_nucleotide_match
153760
157392 137
- .
ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna
ctg889_racon_pilon3
tblastx match_part
157186 157392
263 -
. ID=ctg889_racon_pilon3:hsp:0:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 259 465 -;Gap=M69
ctg889_racon_pilon3
tblastx match_part
157218 157391
284 -
. ID=ctg889_racon_pilon3:hsp:1:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 291 464 -;Gap=M58
ctg889_racon_pilon3
tblastx match_part
157193 157390
241 -
. ID=ctg889_racon_pilon3:hsp:2:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 266 463 -;Gap=M66
ctg889_racon_pilon3
tblastx match_part
156985 157056
87 -
. ID=ctg889_racon_pilon3:hsp:3:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 223 294 -;Gap=M24
ctg889_racon_pilon3
tblastx match_part
156990 157055
96 -
. ID=ctg889_racon_pilon3:hsp:4:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 228 293 -;Gap=M22
ctg889_racon_pilon3
tblastx match_part
156880 156993
166 -
. ID=ctg889_racon_pilon3:hsp:5:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 117 230 -;Gap=M38
ctg889_racon_pilon3
tblastx match_part
156879 156986
154 -
. ID=ctg889_racon_pilon3:hsp:6:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 116 223 -;Gap=M36
ctg889_racon_pilon3
tblastx match_part
156881 156985
141 -
. ID=ctg889_racon_pilon3:hsp:7:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 118 222 -;Gap=M35
ctg889_racon_pilon3
tblastx match_part
153762 153845
128 -
. ID=ctg889_racon_pilon3:hsp:8:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 3 86 -;Gap=M28
ctg889_racon_pilon3
tblastx match_part
153761 153844
134 -
. ID=ctg889_racon_pilon3:hsp:9:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 2 85 -;Gap=M28
ctg889_racon_pilon3
tblastx match_part
153760 153843
137 -
. ID=ctg889_racon_pilon3:hsp:10:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 1 84 -;Gap=M28
ctg889_racon_pilon3
cdna2genome
expressed_sequence_match
153760 157392
2022 +
. ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna
ctg889_racon_pilon3
cdna2genome
match_part 153760
153845 2022
+ .
ID=ctg889_racon_pilon3:hsp:11:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 1 86 +;Gap=M86
ctg889_racon_pilon3
cdna2genome
match_part 155744
155774 2022
+ .
ID=ctg889_racon_pilon3:hsp:12:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 87 117 +;Gap=M31
ctg889_racon_pilon3
cdna2genome
match_part 156881
157055 2022
+ .
ID=ctg889_racon_pilon3:hsp:13:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 118 293 +;Gap=M105 I1 M70
ctg889_racon_pilon3
cdna2genome
match_part 157221
157392 2022
+ .
ID=ctg889_racon_pilon3:hsp:14:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 294 465 +;Gap=M172
ctg889_racon_pilon3
blastx
protein_match 153760
157389 133
+ .
ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA
ctg889_racon_pilon3
blastx
match_part 153760
153846 133
+ .
ID=ctg889_racon_pilon3:hsp:15:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 1 29;Gap=M29
ctg889_racon_pilon3
blastx
match_part 156881
156994 191
+ .
ID=ctg889_racon_pilon3:hsp:16:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 40 77;Gap=M38
ctg889_racon_pilon3
blastx
match_part 156985
157389 314
+ .
ID=ctg889_racon_pilon3:hsp:17:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 75 154;Gap=M19 D35 M4 D20 M57
ctg889_racon_pilon3
protein2genome
protein_match 153760
157389 668
+ .
ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA
ctg889_racon_pilon3
protein2genome
match_part 153760
153845 668
+ .
ID=ctg889_racon_pilon3:hsp:18:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 1 28;Gap=M28 F2
ctg889_racon_pilon3
protein2genome
match_part 155744
155774 668
+ .
ID=ctg889_racon_pilon3:hsp:19:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 29 39;Gap=R2 M11
ctg889_racon_pilon3
protein2genome
match_part 156881
157055 668
+ .
ID=ctg889_racon_pilon3:hsp:20:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 40 97;Gap=M35 I1 M1 F2 M20 F1 F1
ctg889_racon_pilon3
protein2genome
match_part 157221
157389 668
+ .
ID=ctg889_racon_pilon3:hsp:21:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 98 154;Gap=R2 M57
There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?
Thanks for your help.
Patrick Tran Van
Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206