Yannick,
this can also be done directly, by simply reversing the
order of the BLAST search. If you use the genome as the
query, and the ESTs as the database, the resulting file
(using the m8 format) will load directly into Artemis over
the genome.
You will also need to set V=, B= and hspmax= to very large
numbers, so that no results are filtered out by BLAST. There
is also a "span" parameter which should be set to avoid
BLAST removing multiple hits to one part of the genome. By
default BLAST often filters and removes hits without
informing the user.
yours,
Julian Parkhill.
Yannick Wurm wrote:
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
__________________________________
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> - Doctoral student
Department of Ecology and Evolution
http://www.unil.ch/dee/page28685.html
#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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--
Julian Parkhill
Senior Investigator, The Sanger Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SA, UK
Visiting Professor in Microbial Genomics,
University of Oxford
Tel: +44(0)1223 494975, Fax: +44(0)1223 494919
http://www.sanger.ac.uk/Projects/Microbes
http://www.sanger.ac.uk/Teams/faculty/parkhill
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