Hi Newton,<br><br>Have you tried passing the draw_protein option?<br><br> [Polypeptide]<br> feature = polypeptide<br> glyph = transcript<br> draw_protein = 1<br><br>Also check out the "protein" and "translation" glyphs.<br>
<br>The T. cruzi problem sounds like a chado issue -- I will defer to Scott and/or David on this.<br><br>Best,<br><br>Lincoln<br><br><div class="gmail_quote">On Tue, Dec 16, 2008 at 2:01 PM, Newton Vidal <span dir="ltr"><<a href="mailto:nwvidal@gmail.com">nwvidal@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear all,<br> <br>I am starting to work with GMOD and Chado, and I have uploaded genbank files from five different protozoan genomes, using bp_genbank2gff3.pl and gmod_bulk_load_gff3.pl scripts in our local chado v. 1.0 database.<br>
<br>I have run into two major problems when visualizing data with Gbrowse v. 1.69:<br> <br>· The polypeptide feature shows nucleic acid sequence instead of amino acid, when clicked;<br>· For four of the genomes (Leishmania sp. and Trypanosoma brucei) the others features work fine, but for T. cruzi, no data is provided when I click its features.<br>
<br>I have edited chado.conf file to work with my database and added the lines below:<br> <br>[Polypeptide]<br>feature = polypeptide<br>glyph = transcript<br>height = 10<br>key = Polypeptide<br>
bgcolor = green<br> <br>I'm sending attached T. brucei and T. cruzi's GFF files and gbrowse conf file. I have a 80MB dump file and I can share it if needed.<br> <br>Thanks in advance,<br><font color="#888888"> <br>
Newton Vidal<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br><br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>