<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">If you want to try and do this programmatically, you can try libraries like the Gene Annotation Library (GAL) from the Sequence Ontology —> <a href="https://github.com/The-Sequence-Ontology/GAL" class="">https://github.com/The-Sequence-Ontology/GAL</a><div class=""><br class=""></div><div class="">Or if you are looking for visualization or other manipulation you can try one of the GMOD tools —> <a href="http://gmod.org/wiki/Main_Page" class="">http://gmod.org/wiki/Main_Page</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 21, 2020, at 12:38 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div dir="auto" class="">Thanks Carson</div></div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Please how do I assemble the match-part on the match parent? Any special instruction on the maker control file?</div><div dir="auto" class=""><br class=""></div><div class=""><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 21 Aug 2020 at 6:09 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">If you just want a count you can grep for match with tabs at either side —> grep -P “\tmatch\t” file.gff<br class=""><div class=""><br class=""></div><div class="">If you want the model, you need to assemble the match parts onto the match parent.</div></div><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jul 26, 2020, at 11:31 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Hello,</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I am annotating my genome using SNAP after running SNAP twice my GFF has quite a number of </span><span style="font-family:-webkit-standard;font-size:12px" class="">match_part. How can I get an actual match?</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-family:-webkit-standard;font-size:12px" class=""><br class=""></span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-family:-webkit-standard;font-size:12px" class=""><br class=""></span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 890 1003 +;Gap=M114</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">contig_844_pilon_pilon_pilon snap_masked match_part 66719 66729 8.644 + . ID=contig_844_pilon_pilon_pilon:hsp:2866471:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1004 1014 +;Gap=M11</span></div><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel,Ph.D<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">+2348068124819</div><div class="">Publications: </div><div class=""> <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div></div></div></div></div></div><br class=""><br class=""></div></blockquote></div><br class=""></div></blockquote></div></div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">Nnadi Nnaemeka Emmanuel,Ph.D<br class="">Department of Microbiology,<br class="">Faculty of Natural and Applied Science,<br class="">Plateau State University, Bokkos, Plateau State, Nigeria.<br class="">+2348068124819<br class="">Publications: <br class=""> <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><br class=""></div>
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