FW: [Bioperl-l] How to extract promoter region seq from genbank or another source?

[Sam Al-Droubi]

All,
   
  I have found this website http://biowulf.bu.edu/zlab/PromoSer/  that given list of accession numbers, will give you back the promoter regions.  It works very well.  I believe I posted this on the email list after I found it.
   
  

hz5 at njit.edu wrote:
  http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp

Quoting Stefan Kirov :

> Sam,
> You can use MART to convert to ensembl id (in most cases). I don't think
> 
> they support genebank. You can try to use genekeydb 
> (genereg.ornl.gov/gkdb), either download it or use the online converter,
> 
> but my guess is you are not going to get too many ids. One thing I may
> 
> fix in the future, but right now... Still may be worth a try. Look at 
> seqhound too (http://www.blueprint.org/seqhound/index.html).
> Stefan
> 
> Brian Osborne wrote:
> 
> >ENSEMBL experts?
> >
> >------ Forwarded Message
> >From: Sam Al-Droubi 
> >Date: Fri, 14 Oct 2005 14:05:38 -0700 (PDT)
> >To: Brian Osborne 

> >Subject: Re: [Bioperl-l] How to extract promoter region seq from
> genbank or
> >another source?
> >
> >Hi Brian,
> > 
> >Thank you for the response. I looked at it but it seems that enembl
> does
> >not use accession numbers. It seems that they have their own
> numbering
> >scheme. If so how do I get the mapping between the two. If I can't
> get the
> >promoter region sequence then do you know if there is a way I can get
> the
> >entire chromosome sequence? If so, I can then try to find the gene
> within
> >it and then grab the promoter region.
> >I am new to all this so I am sorry if I sound ignorant in this area.
> > 
> >On the surface, it seems that one should be able to do this easily but
> it
> >has not been easy so far.
> > 
> >Thank you. 
> >
> >
> >Brian Osborne 
wrote:
> > 
> >
> >>Sam,
> >>
> >>ensembl may be one solution, I think it provides a good API for these
> sorts
> >>of queries. See the ensembl API documentation for more information
> >>(http://www.ensembl.org/info/software/core/core_tutorial.html).
> >>
> >>Brian O.
> >>
> >>
> >>
> >>On 10/13/05 11:25 AM, "Sam Al-Droubi" wrote:
> >>
> >> 
> >>
> >>>>Hello,
> >>>>
> >>>>I am totally new to BioPerl. I was able to install it and retrieve
> data
> >>>> 
> >>>>
> >>>from
> >>> 
> >>>
> >>>>GenBank. I have a list of accession numbers for genes but I want to
> use
> >>>>BioPerl to get the promoter region (1000 bp before the start of the
> gene).
> >>>>Can someone point me in the right direction on how to accomplish
> this.
> >>>>
> >>>>Tech info: Using bioperl-1.5 on SuSE 9.3 professional machine.
> >>>>
> >>>>Thank you.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>Sincerely, 
> >>>>Sam Al-Droubi, M.S.
> >>>>saldroubi at yahoo.com
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l at portal.open-bio.org
> >>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>> 
> >>>>
> >> 
> >>
> >
> >
> >Sincerely, 
> >Sam Al-Droubi, M.S.
> >saldroubi at yahoo.com
> >
> >------ End of Forwarded Message
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 
> >
> 
> -- 
> Stefan Kirov, Ph.D.
> University of Tennessee/Oak Ridge National Laboratory
> 5700 bldg, PO BOX 2008 MS6164
> Oak Ridge TN 37831-6164
> USA
> tel +865 576 5120
> fax +865-576-5332
> e-mail: skirov at utk.edu
> sao at ornl.gov
> 
> "And the wars go on with brainwashed pride
> For the love of God and our human rights
> And all these things are swept aside"
> 
> _______________________________________________
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> 



=========================================================
Haibo Zhang, PhD
Computational Biology
http://www.cyberpostdoc.org/
Share postdoc information in cyberspace. Welcome your stories, suggestions and 
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Sincerely, 
Sam Al-Droubi, M.S.
saldroubi at yahoo.com