Tim,
thanks for the rapid reply!
I will have a look at the dev version. Sounds interesting.
Regarding the blast tracks. What I do is I generate ORFs using gmHMM or 
prodigal... and blast those in one go limiting 4 hits each. I than postprocess 
these files into embl annotation files using the ORF prediction location and 
the blast info... Looks lik the dev will exactly show the 4x annotation 
feature...hopefully :-)

Will experiment with the hyperlinks....
Cheers
Alex


________________________________________
Van: Tim Carver [t...@sanger.ac.uk]
Verzonden: woensdag 11 april 2012 15:50
To: 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 features in a 'Feature Stack View'.
Currently this is in the development version of Artemis,
http://www.sanger.ac.uk/resources/software/artemis/#development. The option
can be accessed from the 'Display' menu in Artemis.

Artemis does know about some hyperlinked databases defined in the options
file:

hyperlinks = \
  EMBL+SWALL+UniProt+UniProtKB srs_url \
  InterPro http://www.ebi.ac.uk/interpro/ISearch?query= \
  PlasmoDB http://plasmodb.org/plasmodb/servlet/sv?page=gene&source_id= \
  Pfam http://pfam.sanger.ac.uk/family?acc= \
  SMART http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN= \
  Prosite http://www.expasy.org/prosite/ \
  .......

You can add this to the end of that list:

  GI http://www.ncbi.nlm.nih.gov/protein/

so GI numbers (GI:153930843) are then hyperlinked (
http://www.ncbi.nlm.nih.gov/protein/153930843).

Regards
Tim

On 4/11/12 1:49 PM, "Bossers, Alex" <alex.boss...@wur.nl> wrote:

> 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 features to for instance an identified
> ORF? What would be the easiest or best way to accomplish this? Of course
> loading 4 entries for each sequences is cumbersome...
>
> In addition would it be possible to incorporate somehow an embedded link to
> the blasthit identified protein in ENTREZ? Using the gi this should be
> possible to create the link, but can it be functional in Artemis?
>
> thanks
> Alex
>
>
>
> ________________________________________
> Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk]
> namens Tim Carver [t...@sanger.ac.uk]
> Verzonden: dinsdag 13 maart 2012 10:23
> To: artemis-users@sanger.ac.uk
> Onderwerp: [Artemis-users] Artemis and ACT new release
>
> The software releases of Artemis (version 14) and ACT (version
> 11) are now available. The new releases can be downloaded from their home
> pages:
>
> http://www.sanger.ac.uk/resources/software/artemis/
> http://www.sanger.ac.uk/resources/software/act/
>
> As well as further optimisations some of the more notable changes are
> described here:
>
> ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/release_notes.txt
>
> -Tim
>
>
>
> _______________________________________________
> Artemis-users mailing list
> Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>




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