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GA Branch Analysis (Read 4960 times)

Wang_Yan YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 4	GA Branch Analysis May 1^st, 2007 at 9:07am For the last two days, I have submitted my file for GA Branch Analysis several times. Yet the status is always running or waiting, and I have waited for hours without result. The file I submitted is '11'. Can you help me to check the problem? Thank you.
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GA Branch Analysis Reply #1 - May 1^st, 2007 at 11:00am Dear Wang_Yan, The queue has been restarted; all jobs should be processed normally now. Cheers, Sergei
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Wang_Yan YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 4	Re: GA Branch Analysis Reply #2 - May 1^st, 2007 at 8:09pm Dear Sergei, Then how can I retrieve the result of my previous submission? Would you please tell me the link? And I wonder if there is a service that emails me the result, so I don't have to wait online. Thank you for your reply.
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GA Branch Analysis Reply #3 - May 1^st, 2007 at 11:05pm Dear Wang_Yan, GA branch jobs have static URLsfor 96 hours: just look in your browser history and you should be able to find your jobs. We don't have an e-mail notifier set up, but you can always bookmark the page with the job status and come back to it for results later. HTH Sergei
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Wang_Yan

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Re: GA Branch Analysis
Reply #4 - May 2^nd, 2007 at 8:28pm

Dear Sergei,
Thank you for your help. Now I got the result. Yet still some silly questions:
1. How can I determine which color (green/blue/purple/red) stands for positive/negative/neutral seletion? I mean how to read the message, there is a percentage information on the upper right corner.
2. On each of the branch there is a mark of 0.0%, can you tell me what it means?

The website is really new to me, so I am still discovering how to use it.

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Re: GA Branch Analysis
Reply #5 - May 2^nd, 2007 at 9:12pm

Dear Wang_Yan,

Look at the color legend: the first number is the dN/dS value (use this to decide if a branch is selected) for that color, the % value in () shows the proportion of total tree length covered by branches in that color.

Branches are labeled by model-averaged support for seeing dN>dS along that branch. If the value is low then the branch was on average negatively selected. If it is high (e.g. > 95%), then the opposite is true.

You may find it useful to read through the MBE paper which describes the methods as well (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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Wang_Yan YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 4	Re: GA Branch Analysis Reply #6 - May 2^nd, 2007 at 9:37pm Dear Sergei, Then how can I know the corresponding selection form using dN/dS, e.g. if the dN/dS value=0.697(green), 0.062(blue),0.017(purple),0.000(red), respectively?
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Sergei

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Re: GA Branch Analysis
Reply #7 - May 2^nd, 2007 at 10:22pm

Dear Wang_Yan,

dN/dS < 1 - negative selection
dN/dS of about 1 - neutral
dN/dS > 1 - positive selection

In your case all 4 classes are negatively selected, but to different degree.

I would also strongly urge you to review Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

WWW

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