Quickest way to get alignment data for gbrowse_syn
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Quickest way to get alignment data for gbrowse_syn
by michael watson (IAH-C)
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Hello
I'm thinking of creating a test gbrowse_syn installation for a reasonably large metazoan chromosome (and it's orthologue of course). This is about 95Mb in length. So, what's the quickest way to generate an alignment table? I'm pretty sure I'll have to use something really quick, MUMMer perhaps? Or NCBI megablast? I'd then have to parse the data into something that looks like the alignment table. Most of that table I have figured out, except the "bin" column - what is that? Does anyone have any experiences to share? Thanks Mick ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Quickest way to get alignment data for gbrowse_syn
by Dave Clements, GMOD Help Desk-2
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Hi Mick, and everyone else,
This response is more of a non-response, but I'm hoping it will generate some responses with some actual content. I don't know of a particularly easy way to generate alignment data for GBrowse_syn. I don't think Sheldon McKay, the developer of GBrowse_syn, makes any particular recommendation (see http://gmod.org/wiki/GBrowse_syn_Tutorial#Whole_Genome_Alignments). Can anyone out there provide Mick with a recommendation? Thanks, Dave C. On Thu, Nov 5, 2009 at 9:09 AM, michael watson (IAH-C) <michael.watson@...> wrote: > Hello > > I'm thinking of creating a test gbrowse_syn installation for a reasonably large metazoan chromosome (and it's orthologue of course). This is about 95Mb in length. > > So, what's the quickest way to generate an alignment table? > > I'm pretty sure I'll have to use something really quick, MUMMer perhaps? Or NCBI megablast? > > I'd then have to parse the data into something that looks like the alignment table. Most of that table I have figured out, except the "bin" column - what is that? > > Does anyone have any experiences to share? > > Thanks > Mick > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- 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 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Quickest way to get alignment data for gbrowse_syn
by michael watson (IAH-C)
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Hi Dave
Thought I had been forgotten. I am currently running megablast (NCBI) after MUMmer ran out of memory. What I really need is an explanation of what the columns mean in the alignment table(s), including the "bin" column. Thanks Mick ________________________________________ From: gmodhelp@... [gmodhelp@...] On Behalf Of Dave Clements, GMOD Help Desk [help@...] Sent: 09 November 2009 22:44 To: michael watson (IAH-C) Cc: gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] Quickest way to get alignment data for gbrowse_syn Hi Mick, and everyone else, This response is more of a non-response, but I'm hoping it will generate some responses with some actual content. I don't know of a particularly easy way to generate alignment data for GBrowse_syn. I don't think Sheldon McKay, the developer of GBrowse_syn, makes any particular recommendation (see http://gmod.org/wiki/GBrowse_syn_Tutorial#Whole_Genome_Alignments). Can anyone out there provide Mick with a recommendation? Thanks, Dave C. On Thu, Nov 5, 2009 at 9:09 AM, michael watson (IAH-C) <michael.watson@...> wrote: > Hello > > I'm thinking of creating a test gbrowse_syn installation for a reasonably large metazoan chromosome (and it's orthologue of course). This is about 95Mb in length. > > So, what's the quickest way to generate an alignment table? > > I'm pretty sure I'll have to use something really quick, MUMMer perhaps? Or NCBI megablast? > > I'd then have to parse the data into something that looks like the alignment table. Most of that table I have figured out, except the "bin" column - what is that? > > Does anyone have any experiences to share? > > Thanks > Mick > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- 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 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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