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Current FAQs page

Our current FAQs page may be found here.


Frequently asked questions about lab programs (mailman version, blogger version)

Browse FAQ here http://groups.google.com/group/gerstein-lab-faqs?hl=en

Regarding the Science paper titled Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights the numbers in the Table 1 tell something different. According to Table 1, Simultaneously possible interactions have less fraction of same functions, as well as less fraction in co-expression correlation. Can you please clarify?

The table headings unfortunately got switched at some unknown point during copy editing. We have posted a note to that point on our site. Do let me know if you need more help on this!

Regarding the PNAS paper titled Genomic analysis of the hierarchical structure of regulatory networks, I am having trouble understanding the organization of the columns. How was the placement of proteins in columns determined? And what is the purpose behind the duplication of level 1 proteins such as SPT8, and gaps within the columns?

Unfortunately, I think that is a typo when PNAS edited our paper. It is not in our pdf file that we sent to PNAS.

The packing software on molvovdb geometry site working on Mac OS X? If not, can you help with porting it to work on Mac OS X?

There has been problems compiling the program and making it work on Mac OS X. The program was written by a lab member who no longer is available for this. Please continue using the web interface.

MolMovDB: I'd like to have your complete dataset as a benchmark to test the performaces of the methods I'm currently developing.

You can download sets of motion pairs from file list.txt.gz at http://www2.molmovdb.org/wiki/info/index.php/Help_page#Database_formats .

RNA-seq: I had the pleasure of reading your recent article entitled "Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays" in BMC Genomics. My compliments on your article. I am currently working with Affymetrix Human Tiling Arrays to detect novel RNA isoforms and I was looking to borrow from your expertise. I read through your paper but was unable to find details on how the expression analyses of the tiling arrays was performed. If you could let me know what software tool/algorithms were used for this analysis, I'd be most appreciative.

We used min-run max-gap. Similar software at http://genometech.gersteinlab.org/home/home.html .

Pseudogenes in Segmental Duplications : I have recently read this very impressive work ( Segmental duplications in the human genome reveal details of pseudogene formation) and was going through your supplemental tables, which have provided extensive information on status and type of pseudogenes but i did not find strand information (for parent or child) in the spreadsheet. Would it be possible to get strand information for your supplemental datasets.

This information for Ensembl version 48 (the one used in the paper) can be found at http://pseudogene.org/sdpgenes/all_pgenes. Here you will find the pseudogenes in plus and minus directories. Based on the coordinates you have from the supplementary tables you can check the strand of all pseudogenes.


 On 4/8/10 2:22 AM... wrote:
 >                        We  would like to calculate the  packing density
 > within proteins. From your website we found an option to calculate the
 > Voronoi volume of protein atoms. For packing density the volume enclosed
 > within the van der Waal's envelope of the  protein atoms also needs to
 > be calculated. Could you could guide us to such a program available in the
 > public domain which does the above.
 >                                                   with warm regards,

Best to use the "packing-eff" program. (See http://geometry.molmovdb.org/files/libproteingeometry/src-prog3 )

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