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[ADDITION] Batch genome analysis (Read 3064 times)
Sergei
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[ADDITION] Batch genome analysis
Feb 7th, 2007 at 4:02pm
 
Greetings,

I am starting to put together a library of codon based analyses aimed at batch processing of many alignments of orthologs (e.g. for gene-by-gene genome comparison).

Here's something to start this going (take a look at the README file)

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I especially welcome suggestions on what would be useful to have here.

Cheers,
Sergei



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Division of Biomedical Informatics
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University of California San Diego
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Mike
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Re: [ADDITION] Batch genome analysis
Reply #1 - Sep 20th, 2007 at 3:20am
 
Hi Sergei - this looks like just the kind of analysis that I need to do.  Have you continued to develop this since you posted the message in Feb?  If you have more recent code I will be happy to try it out.
cheers
Mike
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Sergei
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Re: [ADDITION] Batch genome analysis
Reply #2 - Sep 20th, 2007 at 6:52am
 
Dear Mike,

Quote:
Hi Sergei - this looks like just the kind of analysis that I need to do.  Have you continued to develop this since you posted the message in Feb?  If you have more recent code I will be happy to try it out.
cheers
Mike


I have streamlined the code and written documentation on how to develop new modules, but I haven't added more modules. The whole pipeline is being integrated into the Galaxy data analysis framework, developed at Penn State U, so eventually there should be quite a few. I updated the original link with the latest files.

Cheers,
Sergei
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sergios-orestis
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Re: [ADDITION] Batch genome analysis
Reply #3 - Apr 20th, 2012 at 5:47pm
 
Dear Sergei,

I was wondering if you had revised/updated GenomeFitters since that 2007 post or if there is another bf we could use. I would like very much to scan for positively selected codons individual alignments (thousands of them) from bacterial NGS data.

Any advice is most welcome, as always.

Best,
Sergios
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