Hi Alex

You can use db_xref. However Artemis should recognise hyperlinks in any
qualifier e.g. /note.

Cheers
Tim

On 4/12/12 9:15 PM, "Bossers, Alex" <alex.boss...@wur.nl> wrote:

> 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
> Onderwerp: RE: Artemis and multiple (interactive) annotation tracks
> 
> 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
>> 
> 
> 
> 
> 
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> 



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