[Gmod-help] RE: [Gmod-gbrowse] Quickest way to get alignment data for gbrowse_syn

[michael watson (IAH-C)]

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 at googlemail.com [gmodhelp at googlemail.com] On Behalf Of Dave Clements, GMOD Help Desk [help at gmod.org]
Sent: 09 November 2009 22:44
To: michael watson (IAH-C)
Cc: gmod-gbrowse at lists.sourceforge.net
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 at bbsrc.ac.uk> 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
>
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