| Thank you Michael - your blasttable2embl is my killer app of the day!
Sharing of insanely useful snippits of bioinformatic code is something there isn't enough of. What would you think about a public repository for "bio-hacks", kind of like http://www.bigbold.com/snippets/ ?
Mit freundlichen Grüssen,
Yannick On Jan 3, 2006, at 6:19 PM, Michael Nuhn wrote: Hi, Yannick! I had this problem some time ago and I have programmed a tool for it: It works like this: Blast your sequences against your favorite genome. Make blast give you a "Hit table". Copy this Hit table into the tool and you will receive an EMBL file which you can use to load into artemis together with your genome sequence. I used this to visualize possible hybridization regions of oligos. Bye, Michael. ----- Original Message ----- Sent: Tuesday, January 03, 2006 2:31 PM Subject: [Artemis-users] Viewing Tblastx database annotation
Dear list,
I have a set of EST sequences which I have tblastx-ed against my favorite genome. Now I would like to view the genome sequence in Artemis, with my EST hits as annotation. After some struggles, I have managed to do the reverse with Artemis 7 on my Mac: load an EST sequence (fasta format) and see where the genome hits (by loading my EST vs. genome tblastx -m8 file)
Is there any way of using artemis to do what I have in mind? The reason is that I basically need to manually go through my blast results, to see how large the corresponding genome ORF might be.
Any other suggestions?
Thanks a bunch for your help,
Yannick __________________________________ Department of Ecology and Evolution
#3106, Biophore, Universite de Lausanne 1015 Lausanne, Switzerland land: +41.21.692.4182 fax: +41.21.692.4165 cell: +41.78.87.87.001
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