Subodh, I'm ccing the Apollo list back into the thread, just for future reference.
Dave C On Wed, Dec 30, 2009 at 11:23 AM, Scott Cain <[email protected]> wrote: > 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 > <[email protected]> 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 <[email protected]> wrote: >> >> From: Dave Clements, GMOD Help Desk <[email protected]> >> Subject: Re: [apollo] Request for annotation protocol using apollo >> To: "subodh srivastava" <[email protected]> >> Cc: [email protected] >> 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 >> <[email protected]> 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 >> >> ________________________________ >> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. >> _______________________________________________ >> apollo mailing list >> [email protected] >> http://mail.fruitfly.org/mailman/listinfo/apollo >> >> >> >> >> -- >> Please keep responses on the list! >> http://gmod.org/wiki/January_2010_GMOD_Meeting >> http://gmod.org/wiki/GMOD_News >> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback >> >> >> ________________________________ >> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > _______________________________________________ > maker-devel mailing list > [email protected] > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org > -- Please keep responses on the list! http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
