Hello all,
I am a big fan of artemis and have ported some of my annotation files
automatically to it.
Currently I am interested in doing multiple genome comparisons. I know I can
use webact or double act to generate big_blast alignments which should be
appropriate for opening in ACT.
However
("\t", @split[11..12], $split[6], $length, '#', '#', @split[2..3],
@split[0..1], '#', $split[7]), "\n";
Hope this helps,
Roy.
Bossers, Alex wrote:
> Hello all,
>
> I am a big fan of artemis and have ported some of my annotation fi
Hi
is there a way to change the spacing/interval of the nt scale in ACT to some
custom value?
Thanks
Alex
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Hi All,
I have been using Artemis/ACT with great joy and have adapted most of my
scripts to output embl compatible data for viewing/annotation by these
tools on whole genomes. This includes blast reports of geneMArk
identified ORFs.
Is there any way to incorporate a working hyperlink or a link to
Hendrik,
experienced the same problem. We wrote some scripts to overcome this problem.
Basically what we do is the following:
1 ) When you have a comparable "reference" genome we determine the synteny of
the contigs by a blat analysis to the reference genome. From that we determine
the possibl
Henrik,
yealing's second option is also how I do it. If you have local blast its not
that bad.
Alex
Van: artemis-users-boun...@sanger.ac.uk namens Yealing
Verzonden: di 11-5-2010 9:57
Aan: Henrik Lantz
CC: artemis-users@sanger.ac.uk
Onderwerp: Re: [Artemis-
Magdalen,
not sure if its supported but we successfully use MUMmer locally (or blast+) to
generate the required comparison files.
Best wishes,
Alex
Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk]
namens Magdalen Lindeberg [m...@cornel
For all interested.
We have written some wrappers to run most of the MUMmer suite functionality
using the galaxy workflow system; It includes a script to convert the MUMmer
comparison file into an Artemis Comparison Tool (ACT) compatible format (~BLAST
crunch).
The wrappers can be found in the
Alternatively (as we do it) we generate an EMBL FT track containing the layout
of contigs (incl any rev complementing and/or linkers). Works quite well for us
and keeps comparison files clean/original.
ALex
-Oorspronkelijk bericht-
Van: artemis-users-boun...@sanger.ac.uk
[mailto:artemis
00917_contig00127"
FT /colour=135 206 250
FT misc_feature29134..29186
=== snip ==
Van: Gowthaman Ramasamy [gowthaman.ramas...@seattlebiomed.org]
Verzonden: donderdag 15 december 2011 15:50
Aan: Bossers,
Hi
I am playing around again with multiple annotation "tracks" in Artemis latest
version locally...
I managed to get BLAST results in the annotation as well as other EMBL FT.
I wondered is it possible to get for let's say a limited BLAST to 4 matches
each entry, to display all those 4 as featur
: Bossers, Alex; artemis-users@sanger.ac.uk
Onderwerp: Re: Artemis and multiple (interactive) annotation tracks
Hi Alex
I am not sure of the best way to limit the number of hits to an ORF but you
may be interested in a new view which is in development at the moment in
Artemis. It displays overlapped
Tim,
which FeaTure key would be best to use when wanting hyperlinked db refs? Is
there some convention?
/db_xref="GI:somenumber"?
Alex
Van: Bossers, Alex
Verzonden: woensdag 11 april 2012 22:31
To: Tim Carver; artemis-users@sanger.ac.uk
Ond
Abhinay
We use MUMmer to generate those comparison files. Scripts available at our free
public galaxy instance (http://galaxy.wur.nl) can convert those for you to
readable files for ACT. Like WebACT does...
Look in the tool section WUR-tools::MUMmer/Artemis. You may find some more
handy things
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