<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Thank you very much for the mail and information.</DIV>
<DIV> </DIV>
<DIV>Can you please explain little more about GFF3 files of organism's genome annotation,</DIV>
<DIV>like, how to creat and example of any small GFF3 files.</DIV>
<DIV> </DIV>
<DIV>I want to use Fgenesh for gene prediction </DIV>
<DIV> </DIV>
<DIV>so the steps will be :</DIV>
<DIV> </DIV>
<DIV>1. genome sequences (in fasta format)</DIV>
<DIV>2. Gene prediction (using Fgenesh)</DIV>
<DIV>3. creation of GFF3 files</DIV>
<DIV>4. uploading in apollo tool </DIV>
<DIV> </DIV>
<DIV>what else..</DIV>
<DIV> </DIV>
<DIV>looking for you reply.</DIV>
<DIV> </DIV>
<DIV>thank you</DIV>
<DIV>regards</DIV>
<DIV>Subodh</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR>********************************************************************************<BR>Subodh K Srivastava <BR>Sr.Lecturer <BR>Amity Institute of Biotechnology (AIB) <BR>Sce-125, Express way <BR>AMITY UNIVERSITY <BR>NOIDA-201304 <BR>UTTAR PRADESH <BR>Mob: +91-9911207970<BR><BR>--- On <B>Wed, 30/12/09, Dave Clements, GMOD Help Desk <I><help@gmod.org></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Dave Clements, GMOD Help Desk <help@gmod.org><BR>Subject: Re: [apollo] Request for annotation protocol using apollo<BR>To: "subodh srivastava" <subodh_srivastava@yahoo.com><BR>Cc: apollo@fruitfly.org<BR>Date: Wednesday, 30 December, 2009, 11:00 PM<BR><BR>
<DIV id=yiv882146230>
<DIV>Hi subodh,<BR></DIV>
<DIV><BR></DIV>
<DIV>Apollo has pretty good documentation that can help you:</DIV>
<DIV><BR></DIV>
<DIV>Apollo Home page:</DIV>
<DIV> <A href="http://apollo.berkeleybop.org/" target=_blank rel=nofollow>http://apollo.berkeleybop.org/</A></DIV>
<DIV><BR></DIV>
<DIV>Apollo User Guide</DIV>
<DIV> <A href="http://apollo.berkeleybop.org/current/userguide.html" target=_blank rel=nofollow>http://apollo.berkeleybop.org/current/userguide.html</A></DIV>
<DIV> This is a great place to start</DIV>
<DIV><BR></DIV>
<DIV>Step by step tutorial on getting Apollo up and running using a starting VMware image.</DIV>
<DIV> <A href="http://gmod.org/wiki/Apollo_Tutorial" target=_blank rel=nofollow>http://gmod.org/wiki/Apollo_Tutorial</A></DIV>
<DIV><BR></DIV>
<DIV>Links to other tutorials</DIV>
<DIV> <A href="http://gmod.org/wiki/Apollo" target=_blank rel=nofollow>http://gmod.org/wiki/Apollo</A></DIV>
<DIV><BR></DIV>
<DIV>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:</DIV>
<DIV><BR></DIV>
<DIV> <A href="http://gbrowse.org/wiki/index.php?title=Special%3ASearch&search=fusarium&go=Go" target=_blank rel=nofollow>http://gbrowse.org/wiki/index.php?title=Special%3ASearch&search=fusarium&go=Go</A></DIV>
<DIV><BR></DIV>
<DIV>Happy new year,</DIV>
<DIV><BR></DIV>
<DIV>Dave C</DIV>
<DIV><BR></DIV>
<DIV class=gmail_quote>On Tue, Dec 29, 2009 at 9:49 AM, subodh srivastava <SPAN dir=ltr><<A href="http://in.mc87.mail.yahoo.com/mc/compose?to=subodh_srivastava@yahoo.com" target=_blank rel=nofollow ymailto="mailto:subodh_srivastava@yahoo.com">subodh_srivastava@yahoo.com</A>></SPAN> wrote:<BR>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<P style="TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>I would like to annotate the Fussarium </FONT><FONT face="Times New Roman" size=3>genome using Apollo. What do I need to do? </FONT>
<P style="TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>may I have the step wise procedure for the annotation and also the file format information and place to download.</FONT>
<P style="TEXT-ALIGN: justify">
<P style="TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>Thank you</FONT>
<P style="TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>subodh</FONT><BR>********************************************************************************<BR>Subodh K Srivastava <BR>Sr.Lecturer <BR>Amity Institute of Biotechnology (AIB) <BR>Sce-125, Express way <BR>AMITY UNIVERSITY <BR>NOIDA-201304 <BR>UTTAR PRADESH <BR>Mob: +91-9911207970</DIV></TD></TR></TBODY></TABLE><BR>
<DIV class=hm>
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