Hi Yan,

Both of the other suggestions are good - I'll also give you another choice to build coordinates before using the "Fetch Sequences -> Extract Genomic DNA" tool to obtain the fasta sequence.


Using your input in BED/Interval format (convert from GFF/GTF if necessary, using the tool "Convert Formats -> GFF-to-BED "), or the first 6 columns if a BED12 (use "Cut" as needed), then run the "Operate on Genomic Intervals -> Get flanks" tool.

  "Region:" Whole feature
  "Location of the flanking region/s:" Both
  "Offset" 0
  "Length of the flanking region(s):" 5000

Your question is similar to this one (the first part, but I thought you might be interested in how to just get the flanks, too).
http://user.list.galaxyproject.org/Get-flanks-version-1-0-0-td4604849.html

Good luck with your project!

Jen
Galaxy team

ps. To search prior questions, please see:
http://galaxy.psu.edu/search/mailinglists/

On 9/23/12 7:00 PM, Yan He wrote:
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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