Question: Suggestions : Developing A Pipe-Line For Scanning Genomic Regions To Identify Known Genomic Elements
2
gravatar for Khader Shameer
9.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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 exist 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.

genome workflow pipeline human • 3.6k views
ADD COMMENTlink written 9.9 years ago by Khader Shameer18k

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?

ADD REPLYlink written 8.7 years ago by brentp23k

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.

ADD REPLYlink written 8.7 years ago by Khader Shameer18k
1
gravatar for Giovanni M Dall'Olio
9.9 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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.

ADD COMMENTlink written 9.9 years ago by Giovanni M Dall'Olio26k

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.

ADD REPLYlink written 9.9 years ago by Khader Shameer18k

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.

ADD REPLYlink written 9.9 years ago by Khader Shameer18k
1
gravatar for Egon Willighagen
9.9 years ago by
Maastricht
Egon Willighagen5.2k wrote:

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

ADD COMMENTlink written 9.9 years ago by Egon Willighagen5.2k

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.

ADD REPLYlink written 9.9 years ago by Khader Shameer18k

Hi, Cyrrile2 link is not working!!

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 5.7 years ago by Prakki Rama2.4k
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