That reply sent slightly prematurely!
I was going to write: Note for this to work, your sequence ids should include a Uniprot identifier, e.g.: FER_CAPAA or seq1|FER_CAPAA|pepper Let us know if that helps! Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: Mungo Carstairs (Staff) Sent: 03 November 2017 11:41:25 To: Vera Belyaeva; jalview-discuss@jalview.org Subject: Re: [Jalview-discuss] sequence feature in Jalview Hello Vera, If I understand your question, you have loaded alignment data from local files (e.g. Fasta) and would like to retrieve Uniprot annotation for these. You can do this from Jalview menu option Web Services | Fetch DB References | Standard Databases (or select Uniprot) Note for this to work, your sequence ids should include a Uniprot identifier, e.g.: FER_CAPAA See section 4.2.1 of the Jalview Manual, at http://www.jalview.org/tutorial/TheJalviewTutorial.pdf, available on the documentation page http://www.jalview.org/about/documentation. [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: jalview-discuss-boun...@jalview.org <jalview-discuss-boun...@jalview.org> on behalf of Vera Belyaeva <vera.belya...@ist.ac.at> Sent: 02 November 2017 21:07:00 To: jalview-discuss@jalview.org Subject: [Jalview-discuss] sequence feature in Jalview Dear all, I have loaded a Uniprot alignment of 2 proteins in Jalview, everything worked perfect. However, I was not able to annotate a certain domain conserved in these 2 proteins (this is a standard domain detected by Uniprot). Is it possible to do it from the alignment file? If not is there another way around? I would greatly appreciate recommendations! Best regards, Vera _______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss The University of Dundee is a registered Scottish Charity, No: SC015096
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