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<p>Dear Maker developper, </p>
<p><br>
</p>
<p>I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :</p>
<p><br>
</p>
<p></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">###</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx translated_nucleotide_match
<span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>157392<span class="Apple-converted-space"> </span>137 <span class="Apple-converted-space">
</span>- <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>157186<span class="Apple-converted-space"> </span>157392<span class="Apple-converted-space">
</span>263 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>157218<span class="Apple-converted-space"> </span>157391<span class="Apple-converted-space">
</span>284 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>157193<span class="Apple-converted-space"> </span>157390<span class="Apple-converted-space">
</span>241 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>156985<span class="Apple-converted-space"> </span>157056<span class="Apple-converted-space">
</span>87<span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>156990<span class="Apple-converted-space"> </span>157055<span class="Apple-converted-space">
</span>96<span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>156880<span class="Apple-converted-space"> </span>156993<span class="Apple-converted-space">
</span>166 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>156879<span class="Apple-converted-space"> </span>156986<span class="Apple-converted-space">
</span>154 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>156881<span class="Apple-converted-space"> </span>156985<span class="Apple-converted-space">
</span>141 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>153762<span class="Apple-converted-space"> </span>153845<span class="Apple-converted-space">
</span>128 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>153761<span class="Apple-converted-space"> </span>153844<span class="Apple-converted-space">
</span>134 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>tblastx match_part<span class="Apple-converted-space">
</span>153760<span class="Apple-converted-space"> </span>153843<span class="Apple-converted-space">
</span>137 <span class="Apple-converted-space"> </span>- <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>cdna2genome <span class="Apple-converted-space">
</span>expressed_sequence_match<span class="Apple-converted-space"> </span>
153760<span class="Apple-converted-space"> </span>157392<span class="Apple-converted-space">
</span>2022<span class="Apple-converted-space"> </span>+ <span class="Apple-converted-space">
</span>. <span class="Apple-converted-space"> </span>ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>cdna2genome <span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>153845<span class="Apple-converted-space"> </span>2022<span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>cdna2genome <span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>155744<span class="Apple-converted-space">
</span>155774<span class="Apple-converted-space"> </span>2022<span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>cdna2genome <span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>156881<span class="Apple-converted-space">
</span>157055<span class="Apple-converted-space"> </span>2022<span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>cdna2genome <span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>157221<span class="Apple-converted-space">
</span>157392<span class="Apple-converted-space"> </span>2022<span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>blastx<span class="Apple-converted-space">
</span>protein_match <span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>157389<span class="Apple-converted-space"> </span>133 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>blastx<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>153846<span class="Apple-converted-space"> </span>133 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>blastx<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>156881<span class="Apple-converted-space">
</span>156994<span class="Apple-converted-space"> </span>191 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>blastx<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>156985<span class="Apple-converted-space">
</span>157389<span class="Apple-converted-space"> </span>314 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>protein2genome<span class="Apple-converted-space">
</span>protein_match <span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>157389<span class="Apple-converted-space"> </span>668 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>protein2genome<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>153760<span class="Apple-converted-space">
</span>153845<span class="Apple-converted-space"> </span>668 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>protein2genome<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>155744<span class="Apple-converted-space">
</span>155774<span class="Apple-converted-space"> </span>668 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>protein2genome<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>156881<span class="Apple-converted-space">
</span>157055<span class="Apple-converted-space"> </span>668 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<p class="p1" style="margin-right: 0px; margin-left: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3
<span class="Apple-converted-space"> </span>protein2genome<span class="Apple-converted-space">
</span>match_part<span class="Apple-converted-space"> </span>157221<span class="Apple-converted-space">
</span>157389<span class="Apple-converted-space"> </span>668 <span class="Apple-converted-space">
</span>+ <span class="Apple-converted-space"> </span>. <span class="Apple-converted-space">
</span>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</span></p>
<br>
<p></p>
<p><br>
</p>
<p>There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?</p>
<p><br>
</p>
<p>Thanks for your help.</p>
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Patrick Tran Van<br>
<br>
Bioinformatician: Lab Chapuisat & Schwander <br>
Department of Ecology and Evolution<br>
University of Lausanne<br>
Lausanne - Switzerland<br>
Office 3206</div>
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