Hi Alex No that isn't the intended behaviour. This view is still in development so thank you for the feedback. I have changed the code so that all frame line features (not just CDS features) should now be separated out. So you should hopefully then see your 4 BLASTCDS features. This is now available from the development download.
Regards Tim On 4/12/12 8:26 PM, "Bossers, Alex" <alex.boss...@wur.nl> wrote: > Tim, > Just played with the latest dev version. Is this normal behaviour? See > screendump? > I have 4 annotations for one specific location (in this case a BLAST > annotation of an ORF). I only see two on the stack view of which the bottem > one seems to have an overlay of the other feature but slightly shifted... > That is correct since that single one is slightly longer. > But I would have expected that features would stack instead of overlap... > Did I miss something? > Alex > > On 4/11/12 9:31 PM, "Bossers, Alex" <alex.boss...@wur.nl> wrote: > >> 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. >> > > > > > -- > 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
