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

[Scott Cain]

Hi Subodh,

I suggest you look at MAKER for doing the prediction: it will handle
most of your work for you (once you have it installed).

  http://www.yandell-lab.org/software/maker.html

Scott


On Wed, Dec 30, 2009 at 2:20 PM, subodh srivastava
<subodh_srivastava at yahoo.com> wrote:
>
> 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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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research