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. _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
