Suggestions : Developing A Pipe-Line For Scanning Genomic Regions To Identify Known Genomic Elements

Question

[Khader Shameer]

I am working on a pipe-line for scanning human genome regions to identify known enhancers, non-coding genes, TFBS, regulatory regions etc. (except coding genes and SNPs). Wondering if something like that exists already? Any recommendations on programs to include in the pipe line for specific applications like TFBS, regulatory elements etc. I have already tried BioMart and Galaxy, but can't find exactly what am looking for.

[brentp]

I am looking for something similar and currently going down the path of: download a bunch of data and the do intersections on each file. Have you found a general tool for this or anything that improves the process?

[Khader Shameer]

No Brent, nothing that covers entire spectrum of genomic elements. Recently I used ENCODE, methylation and ChIP data for some meaningful annotations of non-coding regions.

Answer 1

[Giovanni M Dall'Olio]

Yes there is something for this already. Have a look at Vista which you can use to locate Regulatory Sequences and do comparative analysis, or Transfac for Transcription Factors Binding sites.

[Khader Shameer]

Thanks for your suggestion on rVista, I will try it. I am aware of TRANSFAC, but I don't have access to their new data. They have a restricted public access.

[Khader Shameer]

Tried rVista, but it is a tightly integrated web app. It is not useful for me in its current form. I am downloading the software from here http://pipeline.lbl.gov/software.shtml. Will let you know if I can get something useful.

Answer 2

[Egon Willighagen]

You might find this paper on Cyrrile2 interesting, describing a pipelining environment for genome annotation.

[Khader Shameer]

Thanks Egon. But I am afraid, I wont use this. I am alright at the integration step using a shell script or Perl wrapper. What I am concerned is the selection of tools for analyzing genomic regions. Kind of lost in the options.

[Prakki Rama]

Hi, Cyrrile2 link is not working!!