Re: [gmod-cmap] Additions to CMAP

[Ben F. <fa...@cs...>]

Hi David,

We would certainly be interested in seeing the improvements you've
made.  It's cool to hear that someone else is working with the code.

I would like to see the changes, and then determine how easy it would be
to add them to the current development version (which is a bit different
than the last release (0.14)).

Of course, Ken (and Doreen) have a much greater say in this than I but I
didn't want your offer to stagnate.

Looking forward to working with you,

Ben

On Tue, 2005-08-30 at 22:15, David Schibeci wrote:
> Hi Ken,
> 
> We have been using Cmap installations in our centre since March 2003.  
> One of the requests from our users was to be able to generate  
> consensus maps based on a predefined set of rules developed by  
> Professor Rudi Appels (one of the primary users of our Cmap  
> installation and in charge of curating the data). To this end we have  
> added our own code to the base Cmap install. We think this feature  
> could be of use to the wider community and are interested in  
> contributing to development.
> 
> The generate consensus map script takes two or more maps with  
> correspondences between them, and for each pair of maps:
> * determines the minimum and maximum correspondence between the  
> reference map and the comparison map to maximise the number of  
> features on the comparison map covered by these correspondences
> * performs a linear transform on the features within this selection  
> to scale the features on the correspondence map onto the reference  
> map (all features on the reference map are included)
> * sorts all the reference map and transformed features by name
> * combines any features which have the same name and are 15 cM or  
> less apart, using their averaged start and stop values
> * this forms the consensus map, which can be used as the reference  
> map for additional comparisions
> 
> We're interested in working with you to see if we can contribute this  
> feature. We would of course maintain any code we add. We have also  
> made a few additions to make it easier for admins to maintain the  
> data via the web-based interface (ie import data, make name-based  
> correspondences). These additions provide the same functionality as  
> the command-line cmap_admin.pl and may also be of interest.
> 
> Cheers,
> 
> David Schibeci,
> Andrew Macgregor.
> 
> 
> Centre for Bioinformatics and Biological Computing
> School of Information Technology
> Murdoch University
> Murdoch, WA
> Australia 6150
> 
> 
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