[Artemis-users] Artemis and multiple (interactive) annotation tracks
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 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] 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" 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 > ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] 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" 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
Re: [Artemis-users] Artemis and multiple (interactive) annotation tracks
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" 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
Re: [Artemis-users] Artemis and multiple (interactive) annotation tracks
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" 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" 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
Re: [Artemis-users] Artemis and multiple (interactive) annotation tracks
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" 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" 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" 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 Genom
