Hi Jen,
 
Thanks very much for your help! It is very helpful. However, following your suggestion, what I got is not what I want. Take one sequence for example. The annotation for one scaffold is
C16582GLEANmRNA353850.555898-.ID=OYG_GLEAN_10000001;
C16582GLEANCDS35385.-0Parent=OYG_GLEAN_10000001;
What I got for this scaffold is
>?_C16582_385_5385_-
GCAAACAAGC
>?_C16582_385_5385_-
GCAAACAAGC
I understand that it is trying to get the sequence of the gene downstream from 385-5385, but the sequence is short, so I only get what the scaffold has. I would like to have the upstream+gene+downstream sequence at the same time, not only the upstream or downstream. How can I do this using a galaxy tool? Thanks!
 
Yan
 
 

 
> Date: Mon, 24 Sep 2012 12:26:03 -0700
> From: jen@bx.psu.edu
> To: yanhe83@hotmail.com
> CC: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] extract genome sequence
>
> 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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> --
> Jennifer Jackson
> http://galaxyproject.org