[maker-devel] Why my gene is not annotated ?
Carson Holt
carsonhh at gmail.com
Fri Dec 11 15:49:55 MST 2020
Are you running a trained gene predictor? Perhaps the predictor does not like something about the area, so even with hints, it cannot make a sensible model. Non-canonical splice sites, runs of NNN, internal stop codons (indicates assembly issue in the region) can be the cause.
—Carson
> On Nov 17, 2020, at 9:22 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
>
> 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
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201211/8da86b16/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201211/8da86b16/attachment-0002.p7s>
More information about the maker-devel
mailing list