Yan,
One way to do this is to create an interval file with the new co-ordinates
(+/- 5kb) and then use the Fetch Sequences > Extract genomic DNA tool.
To create a new co-ordinates file, input your annotation file into the
Text Manipulation > Compute tool, using expressions like "c3 = c3-5000" to
get your new co-ordinates. You'll get 2 new columns in the final output
file and then use the Text Manipulation > Cut tool to extract the columns
you need to create an interval file.
Hope this helps.
Cheers,
Graham

Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 24/09/2012 09:02, "Björn Grüning"
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

>Hi Yan,
>
>did you know the tool extractfeat from the EMBOSS suite (its in the
>toolshed)?
>
>I don't know offhand if it can work in batch mode, but its possible to
>add that feature.
>
>Cheers,
>Bjoern
>
>> Hi everyone,
>
>> I have the genome sequence and gene annotation file. Is there a tool
>> on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and
>> genome sequences of the genes (including exons and introns) from the
>> genome sequence? Any suggestions are highly appreciated! Thanks!
>> 
>>  
>> 
>> Yan
>> 
>> 
>> ___________________________________________________________
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>
>-- 
>Björn Grüning
>Albert-Ludwigs-Universität Freiburg
>Institute of Pharmaceutical Sciences
>Pharmaceutical Bioinformatics
>Hermann-Herder-Strasse 9
>D-79104 Freiburg i. Br.
>
>Tel.:  +49 761 203-4872
>Fax.:  +49 761 203-97769
>E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
>Web: http://www.pharmaceutical-bioinformatics.org/
>
>___________________________________________________________
>The Galaxy User list should be used for the discussion of
>Galaxy analysis and other features on the public server
>at usegalaxy.org.  Please keep all replies on the list by
>using "reply all" in your mail client.  For discussion of
>local Galaxy instances and the Galaxy source code, please
>use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>To manage your subscriptions to this and other Galaxy lists,
>please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
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