Custom Cdf Pipeline

Question

[Federico Giorgi]

Dear all,

I have some experience with using the brilliant Custom CDFs from brainarray http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

However, I can't seem to find an already written pipeline for the generation of a completely new CDF (on the website, they describe HOW they generate the custom CDF based on blasts).

What I have is - I think - all that's needed:

• the probe sequences on the microarray
• the CDSs of the genes

Can you help me? Thanks a lot :-)

Federico

Answer 1

[Duff]

Hi Federico

The process used to generate the Brainarray CDFs is outlined in:

Dai, Manhong, Pinglang Wang, Andrew D. Boyd, Georgi Kostov, Brian Athey, Edward G. Jones, William E. Bunney, et al. “Evolving Gene/transcript Definitions Significantly Alter the Interpretation of GeneChip Data.” Nucleic Acids Research 33, no. 20 (October 2005): e175.

This paper (and others) is referenced on the Brainarray website.

Custom CDF files can also be built using bioconductor - I've never done it so I don't know the details but the bioconductor website, mailing list or google may have some suggestions.

Best

Iain

[Federico Giorgi]

Unfortunately no, neither the customcdf mailing list nor the bioc nor google were helpful so far. I guess I will just parse probesvscds blast outpu and generate a de novo CDF. It's a pity, I thought this process would be already automatized by the brainarray team (the concepts are in the paper, but not the code). But a good night at Perl never hurts :-)