[Gmod-help] Re: [apollo] Request for annotation protocol using apollo

[subodh srivastava]

Thank you very much for the mail and information.
 
Can you please explain little more about GFF3 files of  organism's genome annotation,
like, how to creat and example of any small GFF3 files.
 
I want to use Fgenesh for gene prediction 
 
so the steps will be :
 
1. genome sequences (in fasta format)
2. Gene prediction (using Fgenesh)
3. creation of GFF3 files
4. uploading in apollo tool 
 
what else..
 
looking for you reply.
 
thank you
regards
Subodh
 
 
 

********************************************************************************
Subodh K Srivastava 
Sr.Lecturer 
Amity Institute of Biotechnology (AIB) 
Sce-125, Express way 
AMITY UNIVERSITY 
NOIDA-201304 
UTTAR PRADESH 
Mob: +91-9911207970

--- On Wed, 30/12/09, Dave Clements, GMOD Help Desk <help at gmod.org> wrote:


From: Dave Clements, GMOD Help Desk <help at gmod.org>
Subject: Re: [apollo] Request for annotation protocol using apollo
To: "subodh srivastava" <subodh_srivastava at yahoo.com>
Cc: apollo at fruitfly.org
Date: Wednesday, 30 December, 2009, 11:00 PM



Hi subodh,



Apollo has pretty good documentation that can help you:


Apollo Home page:
  http://apollo.berkeleybop.org/


Apollo User Guide
  http://apollo.berkeleybop.org/current/userguide.html
  This is a great place to start


Step by step tutorial on getting Apollo up and running using a starting VMware image.
  http://gmod.org/wiki/Apollo_Tutorial


Links to other tutorials
  http://gmod.org/wiki/Apollo


You will need to get the Fusarium data into a format that Apollo can read (see the user guide for supported formats).  GBrowse.org may have some helpful links:


  http://gbrowse.org/wiki/index.php?title=Special%3ASearch&search=fusarium&go=Go


Happy new year,


Dave C


On Tue, Dec 29, 2009 at 9:49 AM, subodh srivastava <subodh_srivastava at yahoo.com> wrote:







I would like to annotate the Fussarium genome using Apollo. What do I need to do? 
may I have the step wise procedure for the annotation and also the file format information and place to download. 
  
Thank you 
subodh
********************************************************************************
Subodh K Srivastava 
Sr.Lecturer 
Amity Institute of Biotechnology (AIB) 
Sce-125, Express way 
AMITY UNIVERSITY 
NOIDA-201304 
UTTAR PRADESH 
Mob: +91-9911207970



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