SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
problem of gbrowse jiexiong Bioinformatics 3 05-20-2013 12:27 PM
How to convert high version CEL file to low version? lee_sh Bioinformatics 1 05-23-2012 01:47 PM
TopHat and the GFF3 file Ender985 RNA Sequencing 13 05-28-2011 06:02 PM
gbrowse problem user account login/registration apple23 Bioinformatics 5 05-26-2011 06:17 AM
Gbrowse problem??? ptong7 Illumina/Solexa 0 04-07-2009 01:33 PM

Reply
 
Thread Tools
Old 08-06-2012, 10:41 AM   #1
sunfuhui
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

Hi,

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. =(
[GENE]
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
sunfuhui is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO