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Old 08-06-2012, 10:41 AM   #1
Junior Member
Location: athens, ga

Join Date: Jul 2012
Posts: 8
Default Problem with Gbrowse 1.7 old version: it does not recognize the gff3 file well


Could anyone help me figure out the following problem? Thx a lot in advance!
I am trying to update the database of a website which was built on the basis of the flat-file Gbrowse version 1.7.

(1) But after uploading both the gff3 and conf file, I found that the Gbrowse can not recognize some features in the gff3 file.
For example, as to each gene, it has ID, Name and locus_tag in the 9th column
AJKJ01000168 GenBank gene 3811 5214 . - 1 ID=C357_22370;Name=murD;locus_tag=C357_22370
whereas, the Gbrowse will only show its ID.
I want to show it "Name" on the website, too. But my configure file does not work. =(
feature = gene
glyph = arrow
fgcolor = red
linewidth = 2
height = 6
description = sub {
my $feature = shift;
return $feature->attributes("Name");
key = Annotated Genes

Is anything wrong with my codes? ~~~~(T_T)~~~~~~

(2) In addition, I found that I cannot search a gene with its Name.
It feels that the only marker for a gene is its ID.
How can I solve this problem?

Thank you very much again. I am really a green hand in this area. p_(^o^)-q

Ying S
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