What are you currently working on?

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mosare
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What are you currently working on?

Post by mosare » Wed Jul 15, 2015 2:37 am

You don't have to get too specific but I'm curious to know...

What projects is everyone working on?




danfdeblasio
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Re: What are you currently working on?

Post by danfdeblasio » Tue Aug 11, 2015 12:21 am

I'll be the first to start!

I work on improving the quality of protein multiple sequence alignment by taking the choice of alignment parameter choice out of the hands of biologists. In particular, I came up with a method that estimates the accuracy of the output of multiple sequences alignments in the absence of a reference alignment. I then use this estimate to help the user choose the alignment parameters to use for their input (most aligners have lots of tunable alignment parameters that can greatly affect the quality of the alignment).

Specifically, right now I am working on a way to identify well aligned alignment regions (I am estimating if I think columns are in what we call core columns). I am applying this to my accuracy estimator as well as ways to re-align regions that I think may have been aligned using the wrong parameters.

You can find out more about the tool at http://facet.cs.arizona.edu and more about my work at http://dandeblasio.com

How about you?
Dan DeBlasio
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Computational Biology Department
Carnegie Mellon University
Pittsburgh, PA, USA


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Re: What are you currently working on?

Post by mosare » Mon Aug 17, 2015 2:12 am

Is the choice entirely automated or did you leave some room for preference?

Nothing! I just finished up a project base-lining ontology creation methods using next gen data. I will be starting a new project in the winter so I think I'm going to build an app in my "spare" time.




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Re: What are you currently working on?

Post by danfdeblasio » Tue Aug 18, 2015 10:43 pm

So the choice is essentially fixed, but its still a recommendation. There is theoretically room for personal preference based on the universe of parameter choices you select from. The main "preference" for advising the the size of the set (the number of candidate alignments to choose from). You could also produce alignment candidates in whatever manner you want and use Facet to choose among them. I have thought about having some sort of way to have specific parameter sets for different inputs types (high identity alignments, large differences in length, etc) but its something I am not working on.
Dan DeBlasio
ISCB-SC Representative to the ISCB Board of Directors.
ISCB-SC Web Committee, Member
Computational Biology Department
Carnegie Mellon University
Pittsburgh, PA, USA

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