Hello Vaish,
Two good questions there! The short answer is no, not at present, but we can bump and/or raise feature requests for these. Protein / Nucleotide You are right, Jalview 'guesses' nucleotide if the alignment is more than 85% ACGTU - and this doesn't work well with lots of N's. You can force it to nucleotide by running the following Groovy script (Tools | Groovy Console...): def alf = Jalview.alignFrames; alf[0].viewport.alignment.nucleotide=true alf[0].buildColourMenu() If you have multiple alignment windows open you may need to change alf[0] to alf[1] or other index (or loop over all). (The Help page reference to using Jalview.getCurrentAlignFrame() is not correct and won't work.) You should then see that (a) nucleotide colour schemes are offered in the Colour menu and (b) nucleotide substitution matrix is offered in the Calculate Tree or PCA dialog Note this is only a temporary workaround, and would need to be redone, for example, after reloading the data from a saved Jalview project. I will raise a new feature request for this in Jalview. T/U translation For translation of T/U, we have a feature request JAL-1000<https://issues.jalview.org/browse/JAL-1000> on the books. I'll update this for your request. We have a package of work on RNA to get to some time when this may get done, but I can't promise when. The Groovy workaround for this is (adapt as required): def replace = { jalview.datamodel.Sequence sq, String x, String y -> if (sq != null) { str = sq.sequenceAsString str = str.replaceAll(x, y) sq.setSequence(str) } } def alf = Jalview.alignFrames def al = alf[0].viewport.alignment for (seq in al.sequences) { from = 'U' to = 'T' replace(seq, from, to) replace(seq.datasetSequence, from, to) } alf[0].repaint() Let us know if this gives any problems! Best regards, 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: jalview-discuss-boun...@jalview.org <jalview-discuss-boun...@jalview.org> on behalf of Vonyx Crystal <vonyxcrys...@gmail.com> Sent: 13 June 2018 19:02:00 To: jalview-discuss@jalview.org Subject: [Jalview-discuss] Changing Protein to Nucleotide Sequence Hello! I'm trying to align RNA sequences and had a few questions. The first, currently Jalview automatically identifies sequences as DNA or RNA depending on the AGCT content. Is it possible to force Jalview to view a sequence as a nucleotide sequence rather than a protein? (like a setting or command to do so). Our sequences have metacharacters and 'N's in them that confuses Jalview into thinking its a protein. My second question is somewhat simple. Is there a way that Jalview can turn all the 'T's in a sequence (DNA) into 'U's (RNA)? Thanks, Vaish The University of Dundee is a registered Scottish Charity, No: SC015096
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