Re: [XMLPipeDB-developer] OrderedLocusNames for Mycobacterium

[Kevin R. <kev...@ya...>]

Hello Everyone,
I've completed an export for a new database built on GenMAPP Builder 2.0b51, specifically for Mycobacterium tuberculosis, while examining the results in access indeed this new version has retained the RV ordered locus and everything appears in order, however the Tally Engine that I ran still indicates the same results as the former GenMAPP builder, and needs to be updated.
Thank you

--- On Sun, 9/12/10, John David N. Dionisio <do...@lm...> wrote:

From: John David N. Dionisio <do...@lm...>
Subject: Re: [XMLPipeDB-developer] OrderedLocusNames for Mycobacterium
To: "xml...@li..." <xml...@li...>
Date: Sunday, September 12, 2010, 6:59 PM

Greetings,

I've released GenMAPP Builder 2.0b51 to SourceForge; this version seeks to implement the changes described for M. tuberculosis.

Not mentioned in the release notes is also a possible compatibility fix for Windows 7.  Please give this release a try on that operating system also and let me know if it runs.  Try the standard gmbuilder.bat first, and if that doesn't work, try gmbuilder-32bit.bat.  Once we have some definites, I can document it in the next release.

Thanks and enjoy!

John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University



On Sep 8, 2010, at 9:30 PM, Kam Dahlquist wrote:

> Hi,
> 
> Kevin and I looked into the OrderedLocusNames for Mycobacterium 
> tuberculosis today.  We need to revise the query to retreive the IDs.
> 
> We only want to take the IDs of type "orded locus" that begin with 
> "Rv" these IDs are usually followed by four numbers, and sometimes by 
> a letter like a or c, or maybe a .# like .1
> 
> We don't want to take the type "ORF" or type "synonym".
> 
> I think it's also safe to say that we want the default UniProt 
> profile to just take IDs of type "ordered locus" and not "ORF" or "synonym".
> 
> Thanks,
> Kam


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