question about chromosome data construction

[jchl tu]

HI everyone

I am a beginner for Gbrowse and not a professional programmer or some
guys like that. I want to construct my own human genome browse quickly
and easily. but after I`ve read manual, I still don`t know how to
construct data for every single chromosome in one gff and conf file,
for there is always one single region examples in manual, and once
again I don`t know how to draw a chromosome band just like hapmap and
UCSC browse could you please tell me?
Thank you in advances

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[Maureen J. Donlin]

Jchl,

If I understand your question correctly, you can download the genbank
files for each of the human chromosomes.  Assuming you are using some
sort of linux/unix system, you can concatenate them together (cat
*.gbk > human.gbk).  Then uou can generate one gff file using the
bp_genbank2gff2.pl script. You can import them into a mysql database
using the bp_bulk_load.pl script.  Modify the 08_genbank.conf file to
display it.

I hope this helps.

Maureen





On Wed, Sep 9, 2009 at 3:46 AM, jchl tu<tujchl@...> wrote:

> HI everyone
>
> I am a beginner for Gbrowse and not a professional programmer or some
> guys like that. I want to construct my own human genome browse quickly
> and easily. but after I`ve read manual, I still don`t know how to
> construct data for every single chromosome in one gff and conf file,
> for there is always one single region examples in manual, and once
> again I don`t know how to draw a chromosome band just like hapmap and
> UCSC browse could you please tell me?
> Thank you in advances
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
Maureen J. Donlin, Ph.D.

Research Associate Professor
Dept. of Biochemistry & Molecular Biology
Dept. of Molecular Microbiology & Immunology
Saint Louis University School of Medicine
507 Doisy Research Center
314-977-8858

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