Q:

I’m writing to you in connection with your research on the computational tools for the study of residue co-evolution in protein sequences, described in Bioinformatics (2008), http://coevolution.gersteinlab.org

We have a summer internship opportunity here at Dupont Industrial Biosciences (IB) in Palo Alto and the proposed project would involve evaluating different methods for identifying co-evolving residues, so that the suitable method or methods could be applied to proteins and protein families of interest to the company. If this approach is successful, it could help guide future protein engineering efforts here at Dupont IB.

If you happen to know a candidate who would be interested in this internship opportunity, I would welcome your recommendations. I’m in the process of interviewing a few people, but would be glad to talk to additional qualified candidates.

This internship is somewhat unusual because it is not part of a bioinformatics group, so the intern would need to make independent judgments regarding the merits and drawbacks of different approaches and regarding the technical implementation of the project.

My second question is whether there are any terms or conditions associated with using the co-evolution computational tools from your lab? Are the terms different if we were to run these programs on a local computer here within the company (rather than submitting our sequences to the remote server)? I didn’t see any indications to that effect on the coevolution.gersteinlab.org page or in the publication, but it is an important aspect to clarify before using external software within the company, so I hope you can let me know what the rules are or suggest the person I should contact.

A:
I’ll look for an intern. There’s no conditions on the use of this software — it’s open source. Just cite us as described on the permissions page.

Q:
Could you give me a reference for your web site:

http://bioinfo.mbb.yale.edu/align/rankings/?updown=-&subcategory=Folds&category=occurrences&rankby=20genomes&half=30+Highest

A:
thanks for your interest.

The reference is http://papers.gersteinlab.org/papers/partslist-nar

Q:

I hare read with great interest you
recent paper "Classification of human genomic regions based on
experimentally determined binding sites of more than 100
transcription-related factors”.

I am interested in one specific genomic region that I am studying. Based on
the available data in the UCSC browser I believe that this region is an
Enhancer, since it contains the characteristic epigenetic marks, HS-DNA
sites, and binding of a few transcription factors.

I have tried to find the predictions done in your paper for that specific
region. However I have not found a link to the predictions done (maybe I
have just missed it). I think my region should be a BAR and a DRM. Since you
have screened Chip-Seq data from a large number of Transcriptional
regulatory Factors I would be highly interested to know which specific
transcription factors bind to the region. Additionally it would be great to
known if this region belongs to the set of DRM in which you identified a
potential target gene.

Are the results from you study available for download? If not would it be
possible to get the results for a specific region?

A:
see http://encodenets.gersteinlab.org/metatracks

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

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.)