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; firstname.lastname@example.org > 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; email@example.com > 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: firstname.lastname@example.org >> 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 >> Artemisemail@example.com >> 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. > _______________________________________________ Artemis-users mailing list Artemisfirstname.lastname@example.org http://lists.sanger.ac.uk/mailman/listinfo/artemis-users