Thank you Mungo and Jim! I apologize for not being very clear in my question. Thankfully, Jim's last paragraph in the email was exactly what I needed, and my problem is solved :)
Thank you, Kate On Mon, Aug 31, 2020 at 2:59 AM James Procter <j.proc...@dundee.ac.uk> wrote: > Hello Kate. > > Apologies for adding yet another response to Mungo's two suggestions. > > Your email suggests the 'Position 1' you talk about is position '1' of > the alignemnt ruler, which counts columns rather than sequence > positions. If one of your sequences is longer than the others, and there > are no insertions in the other sequences, then the ruler will indeed > reflect the position of that sequence, but Jalview isn't doing anything > special here - just showing the column numbers. > > If you'd like to have the ruler show positions with respect to a > particular sequence, however, then right-click on that sequence's ID and > select the 'Set As Reference' option from the submenu. Now, the > alignment ruler reflects positions with respect to your 'reference' > sequence. > > As Mungo says - if we still haven't worked out what you were asking, > then let us know - but please also let us know if this helped you out ! > > Jim. > > > > On 31/08/2020 09:24, Mungo Carstairs (Staff) wrote: > > Hello Kate, > > > > I'm not quite sure what the question is, so I'll answer two ways. > > > > You can change the order of sequences in the alignment by clicking on > > the sequence name and dragging them up or down. > > > > You can change the start position of a sequence by right-clicking on the > > name, and following the popup menu to > > <Sequence Name> | Edit Name/Description > > and then type the desired /start-end after the sequence name, for example > > myproteinname/20-88 > > If you don't want to do the math(s) to work out the end position, just > > type /20-20 and Jalview will work it out for you. > > > > Position numbering is per sequence, so changing it to "start on a > > different sequence" doesn't make sense, or perhaps I haven't understood > > your question properly. > > > > One more detail: if you want to save your alignment as a Fasta (or other > > format) text file, then check/tick the box for "Append /start-end" for > > the file format in Jalview Preferences' Output options panel. You'll > > find Preferences under the Tools menu. If you don't do this, sequences > > will revert to starting at position 1 after saving and reloading. > > > > I hope that helps, if not please ask again! > > > > Best, > > > > MungoEmail signature > > 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 Kate Kim > > <ki...@msg.ucsf.edu> > > *Sent:* 31 August 2020 04:06 > > *To:* jalview-discuss@jalview.org <jalview-discuss@jalview.org> > > *Subject:* [Jalview-discuss] How to change numbering on my alignment? > > Hello, > > > > I have an alignment of five sequences. Position 1 starts on one of the > > sequences, but I would like to change it to start on a different > > sequence. How can I do this? > > > > Thank you, > > Kate > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > _______________________________________________ > > Jalview-discuss mailing list > > Jalview-discuss@jalview.org > > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > > > > -- > ------------------------------------------------------------------- > Dr JB Procter, Jalview Coordinator, The Barton Group > Division of Computational Biology, School of Life Sciences > University of Dundee, Dundee DD1 5EH, UK. > +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk > >
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