Tag Archives: mg

pseudogenes in bacteria

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Q:

I see you have developed pipelines to look for pseudogenes. Is there someone still working on this problem in your lab?

It turns out there is no good method to find pseudogenes in bacteria, which is perhaps a less challenging problem than in eukaryotes, because of the lack of splicing. There is a real need for such a pipeline because genome degradation is a common pathway to specialization in pathogens. We have hundreds of genomes we would like to put through such a pipeline.

A:
turns out we’ve done pgenes in bacteria and have some old lists available. See :
http://papers.gersteinlab.org/papers/prok-pgenes

permission for access to libproteingeometry-2.3.1

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Q:

I am interested in using the code of "libproteingeometry-2.3.1" to calculate the molecular surface area for my system (the size is less than 50 atoms). Therefore, I would like to get your explicit permission in order to incorporate the code of "libproteingeometry-2.3.1" into the Gaussian 03 program (commercial program) on the lion clusters of PSU. Thanks a lot!!

A:
That’s fine just make sure you credit via cite and URL. -m

Reprint request

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Q:

I would appreciate a copy of your recent article in Genome Biology:
The real cost of sequencing: higher than you think! Genome Biol. 2011 Aug 25;12(8):125.

A:
Thank you for requesting copies of some of my recent
papers. Essentially all of my work is available on-line. Go to:

http://papers.gersteinlab.org

and click on the appropriate "preprint" link. You will be get a
preprint or (if appropriate) journal reprint of the paper you want.
There should be NO password challenges or other barriers. Usually, the
papers are in PDF format but some are in HTML. (Other formats are
available directly from http://papers.gersteinlab.org/e-print.)

Data matrices and R scripts for the paper “Quantifying environmental adaptation of metabolic pathways in metagenomics”

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Q:
With respect to your your metagenomics paper which appeared in PNAS (http://www.pnas.org/content/106/5/1374.long), I was wondering if it is still possible to access the entire (1) environmental features vs. geographic sites and (2) metabolic features vs. geographic sites matricesas used in the paper? Also, is it still possible to access the R scripts that were used in this work?

A:
see http://metagenomics.gersteinlab.org/

probe radius

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Q:


I would like to calculate the solvent accessible surface of certain
proteins. By using your method (online available on
http://helixweb.nih.gov/structbio/basic.html) one can set the probe radius
to maximal size of 1.6 Å. Because I would like to mimic methylene groups as
solvent, the probe radius should be ~1.9 Å (Johnson R.M. et al, Biochemistry
2006, 45, 8507-8515) .
Is there a possibility to increase the probe size radius to 1.9 Å and
calculate the accessible surface using your method?

Question goes here

A:

Your answer here

I think you can do this by downloading the software from
http://www2.molmovdb.org/wiki/info/index.php/Macromolecular_Geometry