Quantification of private information leakage from phenotype-genotype data: linking attacks – do you have slides?

Q:
I am contacting you as I found your paper extremely interesting and very close to the activities I am doing. I would really like to present your work at our weekly lab meeting to my colleagues. Hence, I was wondering if perhaps you have some slides that I could use for this purpose.

A:
see
http://lectures.gersteinlab.org/summary/Genomic-Privacy-n-Individualized-RNAseq-Incompatible-or-Feasible–20161111-i0idash16/
+
other privacy tagged stuff at
http://lectures.gersteinlab.org/summary/

Help with Voronoi software

Q:
I have a protein PDB structure I’ve seen you this text´╝î,I want to use Voronoia software to find the cavity of the protein and the amino acids of the cavity ,Can you help me to analyse it? I want to use the SURFNET software to find my cavity,can you help me to analyse? the following is my protein PDB structure.

A:
My apologies for the confusion, but SURFNET was not written by our group. SURFNET was written by Laskowski. Perhaps you could reach out to that team, and they may be able to help:

https://www.ncbi.nlm.nih.gov/pubmed/8603061
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions.
Laskowski RA1.

If you’re interested in using a similar software, you may want to try our 3V server:
http://3vee.molmovdb.org/

If you experience difficulties using 3V, please do not hesitate to let us know.

ps — By the way, I just ran 3v on your pdb. Feel free to set whatever parameters you like, but I used 2 and 6 as probe radii. See attached results.

Questions about FunSeq2

Q:
Recently, I used FunSeq2 to identify non-coding regulatory variations in my
bladder cancer research. In promoter analysis, I discovered the original
file, gencode.v19.promoter.bed, which downloaded from
http://funseq2.gersteinlab.org/static/data_context2.1.2/gencode/, having the
promoter areas of ranking from 1 to 8979 bp, that was inconsistent with the
definition in your article (promoters defined as -2.5 kb from transcription
starting sites).

So, I checked the process script 3.gencode.process.pl, which was downloaded
from http://funseq2.gersteinlab.org/scripts_dev/ and suited for gencode.v16.
This script generated gencode.v16.promoter.bed
(http://funseq2.gersteinlab.org/static/data_context2.1.0/gencode/), and the
BED file’s 3rd column minus 2nd column all equals 2500 (2.5 Kb). After
comparing, I noticed that the latest gencode.v19.promoter.bed has the
additional 5th column, so I realized the 3.gencode.process.pl script had
been re-edited, but I did’t find the latest version on the internet.
Therefore, I wonder whether the latest 3.gencode.process.pl redefined the
meaning of promoter. If it does, can I get one copy of this script?

A:
The promoter file was derived from PCAWG promoter set, which may consider chromHMM segmentation information. Yao have updated this in the v2.1.2, then I keep it in the latest version. User can replace the right file using their own definition of promoters.

The promoter file included in Funseq 2.1.2 is based on PCAWG consortium’s definition, which considers ChromHMM segmentation information. So it will not be exactly 2kb or 2.5kb upstream of TSS.

Using use the current 1000 genomes reference (Phase4 reference) to use BreakSeq2 to perform SV calling

Q:
We have started a Cloud-based Cancer SV Calling project and would like to use BreakSeq2 to perform SV calling, but would like to use the current 1000 genomes reference (Phase4 reference). Because Breakseq2 relies on the coordinates in the breakpoint library GFF, we were hoping that we could either obtain an updated breakpoint library or some advice on the feasibility of using coordinate liftover (via the available hg19 to Hg38 UCSC chain files) to update the coordinates in the GFF inside the latest library hosted on your lab website at:

http://sv.gersteinlab.org/phase1bkpts/breakseq2_bplib_20150129.zip

We are under a time constraint with regard to the Cloud Compute funding, so we would very grateful if you could reply back soon.

A:
I think the best option right now would be to lift over the coordinates to hg38. Both the GFF and the INS files need to be lifted over (you can use CrossMap which supports GFF). After the liftover, you can check to ensure that the SV lengths were lifted correctly, it might be good to ignore SVs whose lengths after the liftover changed. Note that for the INS file, you will need to write a script to liftover the coordinates in the read-name. You can check out the example on the BreakSeq2 page (http://bioinform.github.io/breakseq2/) for how to run from GFF (you will need both the GFF and the INS file). Hope that helps.

problem with server MolMovDB

Q:
It has been a while i am uploading my pdb files on morph server but did no receive any answer. I have checked both files and the atoms are the same. i am afraid what is the problem??

Is it possible to check my uploaded jobs and tell me what is the error causing the problem? it would be very helpful to solve my pdb files problem. Here is the code of last job 755599-30494.

A:
There seems to be something wrong with your PDB files, because when we try running the single-chain server using other PDB pairs, it seems to work fine with those PDBs. For instance, when running the PDBs attached to this email, the following morph is generated (using Safari to visualize the morph):

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=800501-5588

At first glance, your PDBs do not seem to have chain fields. May we ask how you produced your PDB files? Would it be possible for you to re-build the files with the chain fields set to the letter "A" (or any other arbitrary letter)? Then we will continue from there.

Need help on 3v

Q:
I have been running the channel extraction utility of the 3v and I was able to analyze the results successfully using chimera.

However now I want to run on the multiple files by using the local copy of the program. So I just rerun the calculation for the test case to check if I get the same results as the server. But i am not able to do so. I have tried various option but nothing is seems to be working.

Please let me know if you have any suggestion.

A:
the command that was run is on the server is:

Channel.exe -i 2016.aug31.c64.xyzr -b 10.000 -s 3.000 -t 1.500 -g 1.000 -x -57.519 -y -8.258 -z -52.322 -m 2016.aug31.c64.mrc

Can you compare it to what you were running locally?

Trouble installing libproteingeometry on Ubuntu 12.04

Q1:
I am trying to set up your software package (libproteingeometry) on a lab
desktop. I having trouble during the Make step. After running for a while,
one of the packages is unable to link to the appropriate math header files,
causing make to exit with an error. I am able to understand some C++ coding,
but am not proficient enough to come up with a solution to this problem
independently. I would like to use your program, so is there anyway that you
can put me in contact with someone in your lab who might be able to help me
finish installing this software?

A1:
Apologies again for the delay. May I ask how many structures you plan on running? Customizing libprotgeometry for your machine’s settings may be pretty tricky, especially from our end. If you’re not running too many structures, I’d highly suggest using the Online version of this tool (assuming you’re calculating residue-level packing metrics), linked here:

http://www.molmovdb.org/cgi-bin/voronoi.cgi

Q2:
Unfortunately, I plan on using you program in some molecular dynamics analysis, so the number of structures would be on the order of thousands. I fee like this is too much to run on your server (unless your server has a MD analysis option that I missed, which would be great).

I can send you specific error messages I have upon trying to run the make command. Please let me know what would help you. I saw this error on a forum somewhere where it looked like the problem had been solved, but the solution was not posted.

A2:
Yes, please do send us specific error messages upon trying to run make, as well as any other error messages that you obtain. The more info we have, the better. We’ll try to sort things out. Also, what type of OS is your machine running?

Q3:
I run ubuntu 12.04. I’m pretty sure the system is a converted dell. i5 processor, with nvidia graphics card. I’ll send the error messages in the morning.