Hello,

By no annotation, do you mean species-specific annotation (GTF) was not used? And you want to compare to a protein database like Genbank NR or RefSeq? Then these are the instructions. Please let us know if you had something else in mind.


The sequence extraction can be done on Galaxy Main (if that is where you are working), but the BLAST will need to be run on a local or cloud install. To get set up (instance and data), start here:
http://getgalaxy.org
http://usegalaxy.org/cloud

The BLAST+ wrapper recently moved from the distribution to the Tool Shed, but there are installation tools integrated to help get this into your instance. See the latest News Brief for details (Sept 7, 2012) - these are also good to follow as you maintain your instance:
http://wiki.g2.bx.psu.edu/News
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_07

Questions about local/cloud installs are best directed to the galaxy-...@bx.psu.edu mailing list:
http://wiki.g2.bx.psu.edu/Mailing%20Lists

To extract the transcript sequences, use the tool 'Fetch Sequences -> Extract Genomic DNA'. This will accept a custom reference genome from the history, if you have been using one, by changing the option "Source for Genomic Data:" to "History".

Hopefully this helps,

Jen
Galaxy team

On 9/13/12 10:09 AM, Humberto Boncristiani wrote:
Hi.

I got cuffdiff files with gene differential expression on it. I don't
have the annotation, therefore I need to extract the sequence
information from the genome coordinates and them blast them to identify
those.
How the easiest way to do it?

Thanks.

Humberto



*Dr. Humberto Boncristiani*
National Research Council (NRC) Fellow
Adjunct Research Associate
Department of Biology
Univ. North Carolina at Greensboro
312 Eberhart Bldg
Greensboro, NC 27403, USA.
Tel.:(1) 336-256-2591
Fax: (1) 336-334-5839
email: hum...@gmail.com <mailto:hum...@gmail.com>






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